From d5b282a8c2986a482cdb01409335ec3931959cc4 Mon Sep 17 00:00:00 2001 From: Adam English Date: Sun, 4 Feb 2024 16:35:53 -0500 Subject: [PATCH 1/8] core algo finished faster vcf view similar to -T. Now just to integrate it --- repo_utils/run_unittest.py | 21 +++++++++++++++++++++ truvari/region_vcf_iter.py | 38 ++++++++++++++++++++++++++++++-------- 2 files changed, 51 insertions(+), 8 deletions(-) diff --git a/repo_utils/run_unittest.py b/repo_utils/run_unittest.py index 9c3e66d0..04193a46 100644 --- a/repo_utils/run_unittest.py +++ b/repo_utils/run_unittest.py @@ -5,6 +5,7 @@ import sys import pysam from collections import defaultdict +from intervaltree import IntervalTree # Use the current truvari, not any installed libraries sys.path.insert(0, os.getcwd()) @@ -37,3 +38,23 @@ for entry in v: state = entry.info['include'] == 'in' assert state == truv_ans[truvari.entry_to_key(entry)], f"Bad Boundary {str(entry)}" + +""" +New Region Filtering +""" +vcf_fn = "repo_utils/test_files/variants/boundary_cpx.vcf.gz" +bed_fn = "repo_utils/test_files/beds/boundary_cpx.bed" + +tree = defaultdict(IntervalTree) +with open(bed_fn, 'r') as fh: + for line in fh: + data = line.strip().split() + tree[data[0]].addi(int(data[1]), int(data[2]) + 1) + +vcf = pysam.VariantFile(vcf_fn) +for entry in truvari.region_filter(vcf, tree): + assert entry.info['include'] == 'in', f"Bad in {str(entry)}" + +vcf.reset() +for entry in truvari.region_filter(vcf, tree, False): + assert entry.info['include'] == 'out', f"Bad out {str(entry)}" diff --git a/truvari/region_vcf_iter.py b/truvari/region_vcf_iter.py index aadb330b..c941a875 100644 --- a/truvari/region_vcf_iter.py +++ b/truvari/region_vcf_iter.py @@ -4,7 +4,7 @@ import sys import copy import logging -from collections import defaultdict +from collections import defaultdict, deque from intervaltree import IntervalTree import truvari @@ -168,13 +168,35 @@ def region_filter(vcf, tree, inside=True): """ Given a VariantRecord iter and defaultdict(IntervalTree), yield variants which are inside/outside the tree regions """ - for entry in vcf: - start, end = truvari.entry_boundaries(entry) - m_ovl = list(tree[entry.chrom].overlap(start, end)) - if len(m_ovl) == 1: + for chrom, cur_tree in tree.items(): + cur_tree = deque(sorted(cur_tree)) + try: + cur_intv = cur_tree.popleft() + except IndexError as e: + # region-less chromosome + continue + + for entry in vcf.fetch(chrom): + start, end = truvari.entry_boundaries(entry) + # if start is after this interval, we need the next interval + if start > cur_intv.end - 1: + try: + cur_intv = cur_tree.popleft() + except IndexError as e: + if not inside: + yield entry + continue + # next chromosome + break + + # well before + if end < cur_intv.begin: + if not inside: + yield entry + continue + end_within = truvari.entry_variant_type(entry) != truvari.SV.INS - is_within = truvari.coords_within(start, end, m_ovl[0].begin, m_ovl[0].end - 1, end_within) + is_within = truvari.coords_within(start, end, cur_intv.begin, cur_intv.end - 1, end_within) if is_within == inside: yield entry - elif not inside: - yield entry + From b1f2e019dce2b44e56b5c9062c00893e41e02cf7 Mon Sep 17 00:00:00 2001 From: Adam English Date: Sun, 4 Feb 2024 16:39:30 -0500 Subject: [PATCH 2/8] pylint and test files --- repo_utils/test_files/beds/boundary_cpx.bed | 3 +++ .../test_files/variants/boundary_cpx.vcf.gz | Bin 0 -> 567 bytes .../test_files/variants/boundary_cpx.vcf.gz.tbi | Bin 0 -> 132 bytes truvari/region_vcf_iter.py | 7 +++---- 4 files changed, 6 insertions(+), 4 deletions(-) create mode 100644 repo_utils/test_files/beds/boundary_cpx.bed create mode 100644 repo_utils/test_files/variants/boundary_cpx.vcf.gz create mode 100644 repo_utils/test_files/variants/boundary_cpx.vcf.gz.tbi diff --git a/repo_utils/test_files/beds/boundary_cpx.bed b/repo_utils/test_files/beds/boundary_cpx.bed new file mode 100644 index 00000000..c1af045b --- /dev/null +++ b/repo_utils/test_files/beds/boundary_cpx.bed @@ -0,0 +1,3 @@ +reference 10 20 +reference 110 120 +reference2 10 20 diff --git a/repo_utils/test_files/variants/boundary_cpx.vcf.gz b/repo_utils/test_files/variants/boundary_cpx.vcf.gz new file mode 100644 index 0000000000000000000000000000000000000000..57aba8042e31e71ebdaa0e8c849095b83f6c6d2a GIT binary patch literal 567 zcmb2|=3rp}f&Xj_PR>jW?-+U~9L#HS5O6sEI$U7qq%>9AGGDVtN}OGXUd?^PFnbMi zWSiOFYC(Uq%uAp5n143f7cb3S`aDmy^R!#--u}3l6bHy#^3L%;>@%%nJW(%v^jJVoYzJap8KD4=>CLLpY~oc7J2=^ z;GW&V&d>$*RRXM*&1bXyd2U=ZnWH_a`Bd7~gw*5Oe-7`Ta&C&pz3mIHEpX3U@@-@G z=F^*Pt?>OHfGxx-lH-kIvp$iN_v=3Q;Zxl<2j z9X1efIe)od^VY`6mz?<>*&c5G%f6DU@ljJ|-p?QFCO`0w+Lc^#cVd{f?Y$WLS24?z zUAxa2$gSg6p4E~*XW8TDKlkpdox4BK?Z(l0&rClw^+l}m*0W$?TL0oKcfPv|(=>w$ z{}UT;&5PSz@>qM?i&4wlIHJUCdQ;G=$sMMcB9ag&HfbYqv;it5H)5*jla uH%V#iZrmlKal3JsoW_sFT?#9tn;2dHFt|OPcT$-XGpwW;n87IpL;wIEGX3WO literal 0 HcmV?d00001 diff --git a/repo_utils/test_files/variants/boundary_cpx.vcf.gz.tbi b/repo_utils/test_files/variants/boundary_cpx.vcf.gz.tbi new file mode 100644 index 0000000000000000000000000000000000000000..83718c31d40191a3d68ab768b3438101a9ef638a GIT binary patch literal 132 zcmb2|=3rp}f&Xj_PR>jW=?vV3pHfni5)v2^-86WaP6b4XbaV$@4(bm2JSkXEM|p#j zzhZ|PTif@9pc%YQ)xJ%VEn4diG;mG$sx+HD`1}Edvn@GtyLK>$eHO@4U|?7&V0`x> Q(0F+?d!!kdLAHVc0F cur_intv.end - 1: try: cur_intv = cur_tree.popleft() - except IndexError as e: + except IndexError: if not inside: yield entry continue # next chromosome - break + break # well before if end < cur_intv.begin: @@ -199,4 +199,3 @@ def region_filter(vcf, tree, inside=True): is_within = truvari.coords_within(start, end, cur_intv.begin, cur_intv.end - 1, end_within) if is_within == inside: yield entry - From 3255662181d081e09eaa95417bc6a0827383cb6a Mon Sep 17 00:00:00 2001 From: Adam English Date: Sun, 4 Feb 2024 19:26:36 -0500 Subject: [PATCH 3/8] errors --- repo_utils/run_unittest.py | 11 +++++------ .../test_files/variants/boundary_cpx.vcf.gz | Bin 567 -> 612 bytes .../test_files/variants/boundary_cpx.vcf.gz.tbi | Bin 132 -> 132 bytes truvari/region_vcf_iter.py | 14 ++++++-------- 4 files changed, 11 insertions(+), 14 deletions(-) diff --git a/repo_utils/run_unittest.py b/repo_utils/run_unittest.py index 04193a46..e0f2c3be 100644 --- a/repo_utils/run_unittest.py +++ b/repo_utils/run_unittest.py @@ -27,14 +27,13 @@ state = entry.info['include'] == 'in' assert state == truvari.entry_within(entry, region_start, region_end), f"Bad Boundary {str(entry)}" -v = pysam.VariantFile(vcf_fn) -regions = truvari.RegionVCFIterator(v, includebed=bed_fn) - +regions = truvari.RegionVCFIterator(vcf, includebed=bed_fn) +vcf.reset() truv_ans = defaultdict(lambda: False) -for entry in regions.iterate(v): +for entry in regions.iterate(vcf): truv_ans[truvari.entry_to_key(entry)] = True -v = pysam.VariantFile(vcf_fn) +vcf.reset() for entry in v: state = entry.info['include'] == 'in' assert state == truv_ans[truvari.entry_to_key(entry)], f"Bad Boundary {str(entry)}" @@ -52,7 +51,7 @@ tree[data[0]].addi(int(data[1]), int(data[2]) + 1) vcf = pysam.VariantFile(vcf_fn) -for entry in truvari.region_filter(vcf, tree): +for entry in truvari.region_filter(vcf, tree, True): assert entry.info['include'] == 'in', f"Bad in {str(entry)}" vcf.reset() diff --git a/repo_utils/test_files/variants/boundary_cpx.vcf.gz b/repo_utils/test_files/variants/boundary_cpx.vcf.gz index 57aba8042e31e71ebdaa0e8c849095b83f6c6d2a..b5c7614ef7e452183dd18cb37619a510004da711 100644 GIT binary patch delta 594 zcmV-Y02Wd5Qfj2Um@`-#Ym6Y!V+C0 z7){mYZgtcJGb`(u(tlqyr-T-Ioq3;UK5V;DJv7=}OX8PE;E29Qd8u?cAy){z=X0(QK9HHL6%}k|{RJ$?;8Zdx=6*xU$OC8_2uKQQUdk)Do zJBeZqg@uz$*H18f=M>)q@SKdo_HmyOP}AI8w}=v%uBgJQpKACAe<_VBk*qI8okEMu zMBSq+Nc<;Hgaj>^-$j76HRw?-)kSnTX6cEY)0{;<%L2(nT(I{K5wrWB*)oXT&t}Ka zb-m3GOoXO?@|Xbt03VA81ONa4009360763o07LKoEqV*B>Ldle8*Yq284v zAigC3pq@~W2*JMjI`Tg!CZ2&B@&0TlWsJYJf@l2;d zS_?p;Pusw>R`D2*b zGrldLW@dtAy0Tf~6&^#=CE;`=>)oN8tB4l;9Ee| zU_lQ_mK1?$0$l~Z3k%9Xw?X+jDA5Py3!!`?l&Az~0D&eDXexlg0(dTf2LlK)fJOso gHh_l%XgYw$0|-8V2LyORz=4QwiD9Wekdqh!A7!5rtpET3 literal 567 zcmb2|=3rp}f&Xj_PR>jW?-+U~9L#HS5O6sEI$U7qq%>9AGGDVtN}OGXUd?^PFnbMi zWSiOFYC(Uq%uAp5n143f7cb3S`aDmy^R!#--u}3l6bHy#^3L%;>@%%nJW(%v^jJVoYzJap8KD4=>CLLpY~oc7J2=^ z;GW&V&d>$*RRXM*&1bXyd2U=ZnWH_a`Bd7~gw*5Oe-7`Ta&C&pz3mIHEpX3U@@-@G z=F^*Pt?>OHfGxx-lH-kIvp$iN_v=3Q;Zxl<2j z9X1efIe)od^VY`6mz?<>*&c5G%f6DU@ljJ|-p?QFCO`0w+Lc^#cVd{f?Y$WLS24?z zUAxa2$gSg6p4E~*XW8TDKlkpdox4BK?Z(l0&rClw^+l}m*0W$?TL0oKcfPv|(=>w$ z{}UT;&5PSz@>qM?i&4wlIHJUCdQ;G=$sMMcB9ag&HfbYqv;it5H)5*jla uH%V#iZrmlKal3JsoW_sFT?#9tn;2dHFt|OPcT$-XGpwW;n87IpL;wIEGX3WO diff --git a/repo_utils/test_files/variants/boundary_cpx.vcf.gz.tbi b/repo_utils/test_files/variants/boundary_cpx.vcf.gz.tbi index 83718c31d40191a3d68ab768b3438101a9ef638a..b72f4166551b9db4f120e7ef58a4705946a2cafe 100644 GIT binary patch delta 54 zcmV-60LlM^0fYgNI4lNcFx9{Yp}i)-3_=xGVn7ARdXde8sb^sDU_v$zU0eW*c?dNS M000fR{mYSLARdDg@&Et; delta 54 zcmV-60LlM^0fYgNI4p+uU{aV3LVHbu8H6gXz<>&n^&*=GQ_sL4&4g?oy0`!q^AKtv M005~FGu@G7AWjq&Hvj+t diff --git a/truvari/region_vcf_iter.py b/truvari/region_vcf_iter.py index 04fa82cb..df057952 100644 --- a/truvari/region_vcf_iter.py +++ b/truvari/region_vcf_iter.py @@ -183,17 +183,15 @@ def region_filter(vcf, tree, inside=True): try: cur_intv = cur_tree.popleft() except IndexError: - if not inside: - yield entry - continue - # next chromosome - break + if inside: + break + yield entry # well before if end < cur_intv.begin: - if not inside: - yield entry - continue + if inside: + continue + yield entry end_within = truvari.entry_variant_type(entry) != truvari.SV.INS is_within = truvari.coords_within(start, end, cur_intv.begin, cur_intv.end - 1, end_within) From 4ddaa91cfec401f0221fc16a8bd98ef33ad351fa Mon Sep 17 00:00:00 2001 From: Adam English Date: Mon, 5 Feb 2024 12:02:01 -0500 Subject: [PATCH 4/8] progress --- truvari/region_vcf_iter.py | 50 ++++++++++++++++++++++++++------------ 1 file changed, 34 insertions(+), 16 deletions(-) diff --git a/truvari/region_vcf_iter.py b/truvari/region_vcf_iter.py index df057952..11e20f1f 100644 --- a/truvari/region_vcf_iter.py +++ b/truvari/region_vcf_iter.py @@ -176,24 +176,42 @@ def region_filter(vcf, tree, inside=True): # region-less chromosome continue - for entry in vcf.fetch(chrom): - start, end = truvari.entry_boundaries(entry) + cur_iter = vcf.fetch(chrom) + try: + cur_entry = next(cur_iter) + except StopIteration: + # variant-less chromosome + continue + cur_start, cur_end = truvari.entry_boundaries(cur_entry) + + while True: # if start is after this interval, we need the next interval - if start > cur_intv.end - 1: + if cur_start > cur_intv.end - 1: try: cur_intv = cur_tree.popleft() except IndexError: - if inside: - break - yield entry - - # well before - if end < cur_intv.begin: - if inside: - continue - yield entry - - end_within = truvari.entry_variant_type(entry) != truvari.SV.INS - is_within = truvari.coords_within(start, end, cur_intv.begin, cur_intv.end - 1, end_within) - if is_within == inside: + break + # well before, we need the next entry + elif cur_end < cur_intv.begin: + if not inside: + yield cur_entry + try: + cur_entry = next(cur_iter) + cur_start, cur_end = truvari.entry_boundaries(cur_entry) + except StopIteration: + break + else: + end_within = truvari.entry_variant_type(cur_entry) != truvari.SV.INS + is_within = truvari.coords_within(cur_start, cur_end, cur_intv.begin, cur_intv.end - 1, end_within) + if is_within == inside: + yield cur_entry + try: + cur_entry = next(cur_iter) + cur_stop, cur_end = truvari.entry_boundaries(cur_entry) + except StopIteration: + break + + # if we finished the intervals first, need to flush the rest of the outside entries + if not inside: + for entry in cur_iter: yield entry From 6bc38fe1d06ffb885d95ede2443a58bcc6e408b4 Mon Sep 17 00:00:00 2001 From: Adam English Date: Mon, 5 Feb 2024 15:56:56 -0500 Subject: [PATCH 5/8] region fixing Anytime we're using IntervalTree, we have to add 1 to the end. Anytime we're moving out of IntervalTree, we must remove the one. --- repo_utils/run_unittest.py | 2 +- truvari/bench.py | 2 +- truvari/refine.py | 8 +++----- truvari/region_vcf_iter.py | 13 ++++++++++--- 4 files changed, 15 insertions(+), 10 deletions(-) diff --git a/repo_utils/run_unittest.py b/repo_utils/run_unittest.py index e0f2c3be..ce7981bf 100644 --- a/repo_utils/run_unittest.py +++ b/repo_utils/run_unittest.py @@ -34,7 +34,7 @@ truv_ans[truvari.entry_to_key(entry)] = True vcf.reset() -for entry in v: +for entry in vcf: state = entry.info['include'] == 'in' assert state == truv_ans[truvari.entry_to_key(entry)], f"Bad Boundary {str(entry)}" diff --git a/truvari/bench.py b/truvari/bench.py index a9afa455..67891b3d 100644 --- a/truvari/bench.py +++ b/truvari/bench.py @@ -584,7 +584,7 @@ def check_refine_candidate(self, result): if match.comp is not None: chrom = match.comp.chrom pos.extend(truvari.entry_boundaries(match.comp)) - if has_unmatched and pos: # I don't think I need to confirm pos, but unsure + if has_unmatched and pos: self.refine_candidates.append(f"{chrom}\t{min(*pos)}\t{max(*pos)}") diff --git a/truvari/refine.py b/truvari/refine.py index 56916f21..cadc7132 100644 --- a/truvari/refine.py +++ b/truvari/refine.py @@ -81,7 +81,7 @@ def resolve_regions(params, args): reeval_trees, count = truvari.build_anno_tree(args.regions, idxfmt="") logging.info("%d --regions loaded", count) - return [[chrom, intv.begin, intv.end] + return [[chrom, intv.begin, intv.end - 1] for chrom, all_intv in reeval_trees.items() for intv in sorted(all_intv)] @@ -176,15 +176,14 @@ def recount_variant_report(orig_dir, phab_dir, regions): """ tree = defaultdict(IntervalTree) n_regions = regions[regions["refined"]].copy() - n_regions['start'] -= PHAB_BUFFER - n_regions['end'] += PHAB_BUFFER for _, row in n_regions.iterrows(): - tree[row['chrom']].addi(row['start'], row['end']) + tree[row['chrom']].addi(row['start'], row['end'] + 1) summary = truvari.StatsBox() with open(os.path.join(phab_dir, "summary.json")) as fh: summary.update(json.load(fh)) + # Adding the original counts to the updated phab counts vcf = pysam.VariantFile(os.path.join(orig_dir, 'tp-base.vcf.gz')) tpb = len(list(truvari.region_filter(vcf, tree, False))) summary["TP-base"] += tpb @@ -430,7 +429,6 @@ def refine_main(cmdargs): args.benchdir, 'refine.variant_summary.json')) report = make_region_report(regions) - regions['end'] -= 1 # Undo IntervalTree's correction regions.to_csv(os.path.join( args.benchdir, 'refine.regions.txt'), sep='\t', index=False) with open(os.path.join(args.benchdir, "refine.region_summary.json"), 'w') as fout: diff --git a/truvari/region_vcf_iter.py b/truvari/region_vcf_iter.py index 11e20f1f..4f6dc2d6 100644 --- a/truvari/region_vcf_iter.py +++ b/truvari/region_vcf_iter.py @@ -138,6 +138,8 @@ def build_anno_tree(filename, chrom_col=0, start_col=1, end_col=2, one_based=Fal :type `end_col`: integer, optional :param `one_based`: True if coordinates are one-based :type `one_based`: bool, optional + :param `is_pyintv`: add 1 to end position to correct pyintervaltree.overlap behavior + :type `is_pyintv`: bool, optional :param `comment`: ignore lines if they start with this string :type `comment`: string, optional :param `idxfmt`: Index of column in file with chromosome @@ -174,6 +176,9 @@ def region_filter(vcf, tree, inside=True): cur_intv = cur_tree.popleft() except IndexError: # region-less chromosome + if not inside: + for entry in vcf.fetch(chrom): + yield entry continue cur_iter = vcf.fetch(chrom) @@ -186,10 +191,12 @@ def region_filter(vcf, tree, inside=True): while True: # if start is after this interval, we need the next interval - if cur_start > cur_intv.end - 1: + if cur_start > cur_intv.end: try: cur_intv = cur_tree.popleft() except IndexError: + if not inside: + yield cur_entry # pass this back before flush after the while break # well before, we need the next entry elif cur_end < cur_intv.begin: @@ -207,11 +214,11 @@ def region_filter(vcf, tree, inside=True): yield cur_entry try: cur_entry = next(cur_iter) - cur_stop, cur_end = truvari.entry_boundaries(cur_entry) + cur_start, cur_end = truvari.entry_boundaries(cur_entry) except StopIteration: break # if we finished the intervals first, need to flush the rest of the outside entries - if not inside: + if not inside: for entry in cur_iter: yield entry From da23c3835d86fdea8cf1454d83b3100d590aef87 Mon Sep 17 00:00:00 2001 From: Adam English Date: Mon, 5 Feb 2024 16:43:03 -0500 Subject: [PATCH 6/8] updating tests --- .../refine_output_one/refine.regions.txt | 6 +- .../refine.region_summary.json | 28 +- .../refine_output_three/refine.regions.txt | 108 +-- .../refine.variant_summary.json | 18 +- .../refine_output_two/refine.regions.txt | 6 +- ...> fm_06433b401328232c8c4a2f2278e2fb4c.msa} | 94 +-- ...> fm_09e5224f3ed49d0a0d63118c15970e8f.msa} | 20 +- ...> fm_0a842177b0a019f7a4fb813c41b08d1e.msa} | 20 +- ...> fm_0c8572a4abbd43dfe7727d1bbe104e58.msa} | 22 +- ...> fm_0d2e507e60453c89bd248c945dc7f54d.msa} | 20 +- ...> fm_0dd22c519e7416f2e879bd43c26d9682.msa} | 20 +- ...> fm_157340f8623d37786583821b8bd25147.msa} | 20 +- ...> fm_1c44d23cb30292b3d1f847e04365e588.msa} | 20 +- ...> fm_1d20ababbd3c82b9d4be9155373214aa.msa} | 20 +- ...> fm_1d7c9e595e1b2ef479098d45351d36d3.msa} | 32 +- ...> fm_20bd20e862e124e808d69a4270d4895a.msa} | 20 +- ...> fm_2404771658108744496a59df4a81aa48.msa} | 20 +- ...> fm_241ebaea2bd4d12cce6bff185f492856.msa} | 26 +- ...> fm_24fd8ff0eec7e23320c9f4385933e3f5.msa} | 20 +- ...> fm_29711408027d779b5a2977378e72a9e5.msa} | 20 +- ...> fm_2acb877c85cd2b044d5bd5f0537d9b2e.msa} | 22 +- ...> fm_2b01ba4d781cd0dddb30db4277c8ca9b.msa} | 20 +- ...> fm_2bcd8e5fdfaa68491615ae8e8a2e7e21.msa} | 20 +- ...> fm_2c05a87978c7b4aa656e86b640a18690.msa} | 20 +- ...> fm_2e395a6e1327c3cee2e68d6b7c844cc7.msa} | 20 +- ...> fm_32f6f2dff38622b1e9f06443baeb622f.msa} | 24 +- ...> fm_3309323b7a8f49f7d21f616b3f162df2.msa} | 20 +- ...> fm_351515eae575f51a5c58a89edbda4b09.msa} | 20 +- ...> fm_35335f6151c790b9a47a9350279b1936.msa} | 20 +- ...> fm_373e1d1ae04c109544621b85b6e2768d.msa} | 20 +- .../fm_376415b15834e0e44f2cec357e45842b.msa | 295 -------- ...> fm_37addba43ca0bef896cc3f8296ac4789.msa} | 20 +- ...> fm_37dc1e3da979ee027d03cd84019b4904.msa} | 20 +- ...> fm_3a3d4bda444ca93397f3574b58e71451.msa} | 20 +- .../fm_3a73de403e528810fa08a7607a17d7f5.msa | 115 --- ...> fm_3ba0420a0f6db81c0d76f7ba53ba5226.msa} | 20 +- ...> fm_3d73cc7182161a9c5e90b812c17b9c4a.msa} | 20 +- ...> fm_3f90779dcd8c05402fb060d819c516f1.msa} | 22 +- ...> fm_405fa3f356dead7f68ddb49001c0e603.msa} | 20 +- ...> fm_4248c4ccdcf22249a1ca92c0fca9a551.msa} | 20 +- ...> fm_452bf94642317f3790592594df0a74e2.msa} | 15 +- ...> fm_45f1dc1c7a33a6a5fbb511967c1352d7.msa} | 22 +- .../fm_4857d0eafa15c85843680e3bfaf22f43.msa | 165 ----- ...> fm_499b9b66e7735f3d7b3af193f2b77110.msa} | 20 +- ...> fm_4cdf28703764613af970b6a20a9d76f8.msa} | 20 +- ...> fm_4eee85d5b4dd5f6e65e1aa2a72f439df.msa} | 20 +- ...> fm_50a9c4a3245e4f0c0cab0597a64af000.msa} | 20 +- ...> fm_513fe7d43fe32248d0e906427411d74f.msa} | 20 +- ...> fm_5179b77bf332da7c07500c14adccd838.msa} | 20 +- ...> fm_541535ac45889f61485b69c44137fd45.msa} | 20 +- ...> fm_558c505e413a6398b429691dca26a4ea.msa} | 26 +- ...> fm_5b9c7d30d7119b8ee01d9d2df56da7df.msa} | 20 +- ...> fm_5f56f463de2082f8d7163ff2aada8742.msa} | 20 +- ...> fm_6125f7292d70d0bf730d50e79d9e5f9d.msa} | 20 +- ...> fm_6272ac8c11659a343276a77a33bea482.msa} | 20 +- ...> fm_649eba2ef8750104fb27abd65692f3e5.msa} | 20 +- ...> fm_66112df94acfa8f42760b311b37ff111.msa} | 20 +- ...> fm_69e7c4dc7f053eda2403927861e33459.msa} | 20 +- ...> fm_6ab622358b0189242a15e470f601cb6b.msa} | 20 +- ...> fm_6c3ae6985541ddd1146ec32d22021912.msa} | 20 +- ...> fm_6fecb38e42c1fb0e27f26e0c7db37b3a.msa} | 20 +- ...> fm_71d3a3cbc7c7089cca081c650f00a2a6.msa} | 20 +- ...> fm_7253cbbea437a5ec4d1dc4d570629ba6.msa} | 26 +- ...> fm_7345416d874be507c2785df6e2e9361d.msa} | 20 +- ...> fm_76652f704e7f5d8065ba92e110437e4d.msa} | 30 +- ...> fm_7757219ce7f19ac23c5789d167c1c707.msa} | 20 +- ...> fm_783ef04c1562bdfce45b91b59fe4d678.msa} | 22 +- ...> fm_786136b3c2690bd2db0b1ed0059f1abd.msa} | 20 +- ...> fm_7bb50c57d657828978076072c80f8a1f.msa} | 22 +- ...> fm_7ca10eb32dd50e600280f16b4afb82f5.msa} | 20 +- ...> fm_7d4315446a621c1d4a1d8ccb36fdb130.msa} | 20 +- ...> fm_83e1386bb11a239de07f648aed2478a4.msa} | 20 +- ...> fm_85836283fdfecd2a963f6b695137738c.msa} | 20 +- ...> fm_86dba3a0aeae01ccc8257baa7389c2b2.msa} | 20 +- ...> fm_8a7bc612e0bdea73ad6aea0abc428b43.msa} | 20 +- ...> fm_8e86d26235c230b6c03a21914919f32d.msa} | 20 +- .../fm_8f0a476d665d82b7248a60d8b6288338.msa | 65 -- ...> fm_8f863700689b63e4e012e6bd667b5518.msa} | 20 +- ...> fm_9b9b387681fd363ece224e3813679abe.msa} | 20 +- ...> fm_9e47b8fad37392ee138dfca4c2353754.msa} | 20 +- ...> fm_9e8a807906028744f45dff50046a00aa.msa} | 20 +- ...> fm_a2808b205fb6e4ff2a694b9b59fe99d7.msa} | 24 +- .../fm_a4fa20a9084e2838ff934c5663169e02.msa | 190 ----- ...> fm_a9d398ab39129efb27eabfa2cdf49d07.msa} | 20 +- ...> fm_aaf3284dfcd9e22479f7e2d5c0551083.msa} | 20 +- ...> fm_ac49004ec0dccaa0aa222eebaca554b5.msa} | 20 +- .../fm_ae16a0bdeb31c91e26795edee8ad33fb.msa | 660 ------------------ ...> fm_ae89171a433f770e25870ba2623263b5.msa} | 20 +- ...> fm_b05e3a291363048d6af177602ce2b043.msa} | 20 +- ...> fm_b179a5501273075e792cbf44d023019b.msa} | 20 +- ...> fm_b206928da83df6d728521bb51cfc7a4d.msa} | 20 +- ...> fm_b4b25fe75fa812465ce27c19d1fe0ff9.msa} | 20 +- ...> fm_b592bd7606102ee30703461d14728bdd.msa} | 20 +- ...> fm_b8963eabf50fbefd5fbf150779abc34d.msa} | 20 +- ...> fm_bb633e8a0fe19e3e0ef87827050edb6d.msa} | 20 +- ...> fm_bb7fd33627eeebb611fd58a76e4c129f.msa} | 20 +- .../fm_bbc70dbaa5d67ccdda8d60a17b075dca.msa | 295 ++++++++ ...> fm_bd402172ece6674cf9fbe88768975d74.msa} | 20 +- ...> fm_c00504a27ac55beec570218a4eedf56f.msa} | 20 +- ...> fm_c09854a1826e6b88567130408713a7f9.msa} | 28 +- ...> fm_c3ca784845992e7f185ad2e6a992de0e.msa} | 24 +- ...> fm_c50e1186af8d764e9f4a7ebc3e6ca294.msa} | 20 +- ...> fm_c84764c85e3bc2208c93471f25974884.msa} | 20 +- ...> fm_c8767647c15df9e79d6194de26f7cdc5.msa} | 491 ++++++------- ...> fm_ce6ba4dc0f8a352c89d3dfc839c96d2e.msa} | 20 +- ...> fm_cea716cb5fb96bc6d8bf0051a8d70890.msa} | 26 +- ...> fm_cf9425969f7f5ed38f54639e08586a04.msa} | 20 +- ...> fm_d2242ccd448a7c982cfcff72641d3495.msa} | 20 +- ...> fm_d4b126e5900cc00f6c75e82b4be27559.msa} | 20 +- ...> fm_d68e9f67e20c4afd7f0f9e6fada0a063.msa} | 26 +- ...> fm_d758d8d416dd205a6f2a3a988afe6ca4.msa} | 20 +- ...> fm_d7c982150b9084cabc20a2d51cc2fab7.msa} | 34 +- .../fm_d82a691e489dc8fab00bca3d0d072f7e.msa | 65 -- ...> fm_d83685774be2675f1a182646478490ed.msa} | 20 +- ...> fm_da9e583f8bb0c9329678fe2798c29f69.msa} | 15 +- ...> fm_ddb507ec4de0d55fd44561115d512b4c.msa} | 20 +- ...> fm_ddb6122dabcdfbfdfd1b60aa0d3cffd6.msa} | 20 +- ...> fm_df55c8c1ea86802a42a7e9b21d75a6f1.msa} | 20 +- ...> fm_e449e9cc3dfd676b949352d747ef2fae.msa} | 20 +- ...> fm_e595ac0692ae672cf3ea7a03e1e6ad6c.msa} | 20 +- ...> fm_e7315f7330dde260068b31e9e14647d0.msa} | 20 +- ...> fm_e98e8b7a2d661c3ba62b21a0dbc4f7d7.msa} | 20 +- ...> fm_ed1042b42c059891aecf75a626d0d1a8.msa} | 20 +- ...> fm_ed11e856d3a32487f771047b0b77f027.msa} | 20 +- ...> fm_edce4871de28f10080aaa834a9139704.msa} | 20 +- ...> fm_f421dd5eadc752e68b598f461ab861a8.msa} | 20 +- ...> fm_f5ab8103fdc862862724ddfcfe43644a.msa} | 20 +- ...> fm_f80b3949aaede63b2c726a14abd6e835.msa} | 20 +- ...> fm_fb52ef3187571c67509303c4c8e9c08d.msa} | 20 +- ...> fm_fc40819c3b411d6b2869794670b475f9.msa} | 20 +- ...> fm_fd198272bc91bdb42e2dbb32cc9c9935.msa} | 20 +- .../fm_fdcb2c8d04f052ec0422554bbca6ba2d.msa | 165 +++++ .../fm_ff0ae7d50dec8afd13f0c22741c4925e.msa | 660 ++++++++++++++++++ ...> fm_ff5bbed9fc29f7f0637d3929908a94a3.msa} | 20 +- truvari/refine.py | 2 +- 135 files changed, 2708 insertions(+), 3148 deletions(-) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_ad2c051e81d70fcd18bbddaf87dc9140.msa => fm_06433b401328232c8c4a2f2278e2fb4c.msa} (77%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_36dc8f9607000ef7378ba372de940929.msa => fm_09e5224f3ed49d0a0d63118c15970e8f.msa} (84%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_c42f829bb3fad0eeedf846ea3be67cc8.msa => fm_0a842177b0a019f7a4fb813c41b08d1e.msa} (95%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_9be1536e40a58a7128ddc75d12940a3e.msa => fm_0c8572a4abbd43dfe7727d1bbe104e58.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_2f584d342cd0122481374518f9e81904.msa => fm_0d2e507e60453c89bd248c945dc7f54d.msa} (93%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_be4bf563ccc78c76f28205e487e0c322.msa => fm_0dd22c519e7416f2e879bd43c26d9682.msa} (92%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_ae2bc435a754945d8db9c5a5fad60896.msa => fm_157340f8623d37786583821b8bd25147.msa} (95%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_34829e853039a0b83260fb740af39cda.msa => fm_1c44d23cb30292b3d1f847e04365e588.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_afe59e2c01695d7d2653b661248a80ef.msa => fm_1d20ababbd3c82b9d4be9155373214aa.msa} (86%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_7051e6b8ca568da2ec784100ee158134.msa => fm_1d7c9e595e1b2ef479098d45351d36d3.msa} (75%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_94d9fc221f90d8b60251faa405fdfde1.msa => fm_20bd20e862e124e808d69a4270d4895a.msa} (94%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_f949c02c5b00935cf4bd4b3c660a5ded.msa => fm_2404771658108744496a59df4a81aa48.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_717cdf145eb3b53da7ad74d00c183277.msa => fm_241ebaea2bd4d12cce6bff185f492856.msa} (94%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_e19b79eecb589d0faff3fd8eba62aeef.msa => fm_24fd8ff0eec7e23320c9f4385933e3f5.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_c35059068940421b229c17e87e720ab8.msa => fm_29711408027d779b5a2977378e72a9e5.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_9b6ec2bc5fb37634cbfbb07c76684bcf.msa => fm_2acb877c85cd2b044d5bd5f0537d9b2e.msa} (95%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_141ad6632a3577b19e9a4616ecdf6bbe.msa => fm_2b01ba4d781cd0dddb30db4277c8ca9b.msa} (97%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_e0a1b90b66779bb5b8c7086145d6f100.msa => fm_2bcd8e5fdfaa68491615ae8e8a2e7e21.msa} (83%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_dd8b054c3bcd4f4a22fdac0fc01760de.msa => fm_2c05a87978c7b4aa656e86b640a18690.msa} (88%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_0b1f7552f96468523661603cd4269fe6.msa => fm_2e395a6e1327c3cee2e68d6b7c844cc7.msa} (95%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_a9fdcb29d10f9c256c49525ef4fab80f.msa => fm_32f6f2dff38622b1e9f06443baeb622f.msa} (88%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_6147414e8642b5c9ece9fffa3cd6290f.msa => fm_3309323b7a8f49f7d21f616b3f162df2.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_02b73a4f2fb9c7243d2ae74002dc5b27.msa => fm_351515eae575f51a5c58a89edbda4b09.msa} (92%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_bd2f885276994e61366fc4ae806bc3c9.msa => fm_35335f6151c790b9a47a9350279b1936.msa} (93%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_b6f4c42dfe3dd25d3029d99aa8472281.msa => fm_373e1d1ae04c109544621b85b6e2768d.msa} (93%) delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_376415b15834e0e44f2cec357e45842b.msa rename repo_utils/test_files/external/fake_mafft/lookup/{fm_d27af66810a53f2070224212487e9431.msa => fm_37addba43ca0bef896cc3f8296ac4789.msa} (97%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_19907622767ec08f4f2a547410d2ecfb.msa => fm_37dc1e3da979ee027d03cd84019b4904.msa} (95%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_392581e26c6c6574757f793b72e768f0.msa => fm_3a3d4bda444ca93397f3574b58e71451.msa} (95%) delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_3a73de403e528810fa08a7607a17d7f5.msa rename repo_utils/test_files/external/fake_mafft/lookup/{fm_946b797ceaa32d6c1b711e085ad7903e.msa => fm_3ba0420a0f6db81c0d76f7ba53ba5226.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_4dff1cfc21c902e0e7568be207ccbd40.msa => fm_3d73cc7182161a9c5e90b812c17b9c4a.msa} (94%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_3570b2394a58b5622e26496d8c6f1a42.msa => fm_3f90779dcd8c05402fb060d819c516f1.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_5c074fb37f70d5e11502be5c009c13e2.msa => fm_405fa3f356dead7f68ddb49001c0e603.msa} (95%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_8d91e35548435d3392527d244ebe8371.msa => fm_4248c4ccdcf22249a1ca92c0fca9a551.msa} (98%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_ff308abc6d0e72bcf1670b2c17001984.msa => fm_452bf94642317f3790592594df0a74e2.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_2783f53858aad63825027bab32e6c3bb.msa => fm_45f1dc1c7a33a6a5fbb511967c1352d7.msa} (94%) delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_4857d0eafa15c85843680e3bfaf22f43.msa rename repo_utils/test_files/external/fake_mafft/lookup/{fm_69e3cd763dbc4a7d135dbecb492d8b86.msa => fm_499b9b66e7735f3d7b3af193f2b77110.msa} (99%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_686d29fdc617f6ce5cb3c1f76ee016c0.msa => fm_4cdf28703764613af970b6a20a9d76f8.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_9f052ef8e75238e8dd45906b8a291987.msa => fm_4eee85d5b4dd5f6e65e1aa2a72f439df.msa} (97%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_69a6cc9af825b6514565ccdd59336cd0.msa => fm_50a9c4a3245e4f0c0cab0597a64af000.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_bd5862045dd8751a6c83a3c3d6321d88.msa => fm_513fe7d43fe32248d0e906427411d74f.msa} (90%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_14df5b1a78900153927390d7bafee41c.msa => fm_5179b77bf332da7c07500c14adccd838.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_c95ab5f466d7144d537fb37124016439.msa => fm_541535ac45889f61485b69c44137fd45.msa} (97%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_efa1c6acccfa7bcd26ee40e0acbbc623.msa => fm_558c505e413a6398b429691dca26a4ea.msa} (79%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_b9d356b09aad1b84d7626c820eace838.msa => fm_5b9c7d30d7119b8ee01d9d2df56da7df.msa} (93%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_918ac60720a8b1e5a939e5ef71c3dd30.msa => fm_5f56f463de2082f8d7163ff2aada8742.msa} (89%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_d00295e693e29721bd316e2a98d6b49d.msa => fm_6125f7292d70d0bf730d50e79d9e5f9d.msa} (92%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_04f59078ccc583035a295f8ad3526dbf.msa => fm_6272ac8c11659a343276a77a33bea482.msa} (96%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_be2ece84b9803ee6d8b5da47e0f1328a.msa => fm_649eba2ef8750104fb27abd65692f3e5.msa} (90%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_709f39dc3727958f3af64bf428a7aa8c.msa => fm_66112df94acfa8f42760b311b37ff111.msa} (88%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_16a9570a0bae9b86665a101c47ea2a7e.msa => fm_69e7c4dc7f053eda2403927861e33459.msa} (94%) rename repo_utils/test_files/external/fake_mafft/lookup/{fm_b4b5ccc01de0310c6839be1682c17fae.msa => 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repo_utils/test_files/external/fake_mafft/lookup/{fm_0e637d93ff26bf168ee302bf13d84ca8.msa => fm_ff5bbed9fc29f7f0637d3929908a94a3.msa} (90%) diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt index 4c665b54..41bfa0b8 100644 --- a/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt +++ b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt @@ -43,7 +43,7 @@ chr20 19663366 19663526 2 2 0 0 False 2 2 0 0 TP chr20 20295955 20296565 2 2 2 1 True 3 3 0 0 TP chr20 20320285 20320579 1 1 2 1 True 1 1 0 0 TP chr20 20337200 20337707 1 1 6 2 True 3 3 0 0 TP -chr20 20354570 20358323 7 7 9 1 True 14 14 0 0 TP +chr20 20354570 20358323 7 7 9 1 True 16 16 0 0 TP chr20 20458640 20458937 2 2 0 0 False 2 2 0 0 TP chr20 21120212 21120539 2 2 1 0 True 1 1 0 0 TP chr20 21721174 21721735 2 2 1 0 True 3 3 0 0 TP @@ -133,7 +133,7 @@ chr20 58694862 58695411 2 2 0 0 False 2 2 0 0 TP chr20 59383804 59385235 3 3 2 0 True 4 4 0 0 TP chr20 59442036 59442273 2 2 0 0 False 2 2 0 0 TP chr20 60087391 60087965 2 2 0 0 False 2 2 0 0 TP -chr20 60314330 60315020 2 2 2 0 True 6 6 0 0 TP +chr20 60314330 60315020 2 2 2 0 True 5 5 0 0 TP chr20 60600107 60600320 1 1 0 0 False 1 1 0 0 TP chr20 60702942 60703115 2 2 2 1 True 3 3 0 0 TP chr20 60764031 60764634 2 2 0 0 False 2 2 0 0 TP @@ -155,7 +155,7 @@ chr20 61723833 61724244 1 1 0 0 False 1 1 0 0 TP chr20 61744188 61744654 2 2 1 0 True 2 2 0 0 TP chr20 61783403 61784839 3 3 1 0 True 4 4 0 0 TP chr20 61919676 61921374 2 2 0 0 False 2 2 0 0 TP -chr20 62057573 62059139 1 1 3 1 True 8 8 0 0 TP +chr20 62057573 62059139 1 1 3 1 True 7 7 0 0 TP chr20 62212844 62213874 4 4 0 0 False 4 4 0 0 TP chr20 62270279 62271094 1 1 3 1 True 4 4 0 0 TP chr20 62317837 62318459 2 2 0 0 False 2 2 0 0 TP diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json b/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json index 6003cac7..a550c76d 100644 --- a/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json +++ b/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json @@ -1,18 +1,18 @@ { - "TP": 17, - "TN": 6, - "FP": 23, + "TP": 19, + "TN": 10, + "FP": 17, "FN": 58, - "base P": 76, - "base N": 16, - "comp P": 85, - "comp N": 7, - "PPV": 0.2, - "TPR": 0.2236842105263158, - "TNR": 0.375, - "NPV": 0.8571428571428571, - "ACC": 0.25, - "BA": 0.2993421052631579, - "F1": 0.2111801242236025, + "base P": 78, + "base N": 14, + "comp P": 81, + "comp N": 11, + "PPV": 0.2345679012345679, + "TPR": 0.24358974358974358, + "TNR": 0.7142857142857143, + "NPV": 0.9090909090909091, + "ACC": 0.31521739130434784, + "BA": 0.47893772893772896, + "F1": 0.2389937106918239, "UND": 0 } \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt index ae958d94..8a5068b2 100644 --- a/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt +++ b/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt @@ -1,93 +1,93 @@ chrom start end in_tpbase in_tp in_fn in_fp refined out_tpbase out_tp out_fn out_fp state -chr20 278929 279069 3 3 1 0 False 3 3 1 0 FN -chr20 641912 642420 3 3 2 0 False 3 3 2 0 FN -chr20 2240960 2241290 1 1 5 1 True 1 1 4 1 FN,FP -chr20 4032357 4033228 2 2 2 1 True 1 1 2 1 FN,FP -chr20 5040476 5040477 0 0 0 2 False 0 0 0 2 FP -chr20 5041941 5042268 1 1 1 1 True 2 2 0 0 TP +chr20 278929 279069 2 3 1 0 False 2 3 1 0 FN +chr20 641912 642420 2 3 2 0 False 2 3 2 0 FN +chr20 2240960 2241290 0 1 5 1 True 1 1 4 1 FN,FP +chr20 4032357 4033228 2 1 2 1 True 0 0 2 1 FN,FP +chr20 5040476 5040477 0 0 0 0 False 0 0 0 0 TN +chr20 5041941 5042268 1 1 1 0 False 1 1 1 0 FN chr20 7720952 7720968 1 1 1 0 False 1 1 1 0 FN -chr20 8661944 8662119 1 1 3 1 True 2 2 0 0 TP +chr20 8661944 8662119 0 1 2 1 True 2 2 0 0 TP chr20 10802727 10802844 1 1 1 0 False 1 1 1 0 FN -chr20 13848272 13848544 3 3 1 0 False 3 3 1 0 FN -chr20 14862054 14862644 5 5 5 1 True 3 3 1 0 FN -chr20 16257854 16259205 2 2 2 0 False 2 2 2 0 FN +chr20 13848272 13848544 2 2 1 0 False 2 2 1 0 FN +chr20 14862054 14862644 4 4 5 1 True 3 3 1 0 FN +chr20 16257854 16259205 2 2 1 0 False 2 2 1 0 FN chr20 16395201 16395373 3 3 1 0 False 3 3 1 0 FN chr20 17081293 17081365 2 2 1 0 False 2 2 1 0 FN chr20 18209139 18210134 3 3 2 1 True 3 3 0 1 FP -chr20 20296014 20296330 2 2 2 1 True 5 5 0 0 TP -chr20 20320339 20320519 1 1 2 1 True 3 3 0 0 TP +chr20 20296014 20296330 1 1 2 1 True 4 4 0 0 TP +chr20 20320339 20320519 0 1 2 1 True 3 3 0 0 TP chr20 20337285 20337624 1 1 6 2 True 1 1 0 0 TP -chr20 20354912 20355435 3 3 1 0 False 3 3 1 0 FN -chr20 20356530 20357810 4 4 8 1 True 8 8 2 0 FN +chr20 20354912 20355435 2 2 1 0 False 2 2 1 0 FN +chr20 20356530 20357810 2 3 8 1 True 8 8 2 0 FN chr20 21120298 21120461 2 2 1 0 False 2 2 1 0 FN -chr20 21721451 21721646 2 2 1 0 False 2 2 1 0 FN -chr20 22082266 22083905 4 4 3 1 True 3 3 4 1 FN,FP -chr20 23155578 23155857 3 3 2 2 True 3 3 1 1 FN,FP +chr20 21721451 21721646 0 2 1 0 False 0 2 1 0 FN +chr20 22082266 22083905 3 3 3 1 True 3 3 4 1 FN,FP +chr20 23155578 23155857 3 3 1 2 True 3 3 1 1 FN,FP chr20 23560939 23561098 1 1 2 2 True 2 2 0 0 TP chr20 24408073 24408820 3 3 1 0 False 3 3 1 0 FN chr20 24682066 24682125 2 2 1 0 False 2 2 1 0 FN -chr20 25781790 25781791 0 0 0 1 False 0 0 0 1 FP -chr20 32723044 32723045 0 0 1 0 False 0 0 1 0 FN -chr20 34235898 34235981 0 0 2 1 True 2 2 0 0 TP +chr20 25781790 25781791 0 0 0 0 False 0 0 0 0 TN +chr20 32723044 32723045 0 0 0 0 False 0 0 0 0 TN +chr20 34235898 34235981 0 0 1 1 True 1 1 0 0 TP chr20 35539212 35539582 4 4 1 0 False 4 4 1 0 FN chr20 35580686 35580756 1 1 2 1 True 1 1 2 1 FN,FP chr20 37361785 37361886 2 2 1 0 False 2 2 1 0 FN -chr20 38123799 38124003 2 2 1 4 True 1 1 2 3 FN,FP +chr20 38123799 38124003 0 1 1 4 True 1 1 2 3 FN,FP chr20 38463997 38464344 2 2 2 0 False 2 2 2 0 FN -chr20 41196370 41196495 3 3 1 0 False 3 3 1 0 FN +chr20 41196370 41196495 2 3 1 0 False 2 3 1 0 FN chr20 41257714 41258003 0 0 0 1 False 0 0 0 1 FP -chr20 44764150 44764203 2 2 1 0 False 2 2 1 0 FN -chr20 45600655 45600695 2 2 2 0 False 2 2 2 0 FN -chr20 48449794 48450385 4 4 2 0 False 4 4 2 0 FN +chr20 44764150 44764203 0 1 1 0 False 0 1 1 0 FN +chr20 45600655 45600695 0 2 2 0 False 0 2 2 0 FN +chr20 48449794 48450385 4 4 1 0 False 4 4 1 0 FN chr20 49834182 49834469 2 2 1 0 False 2 2 1 0 FN -chr20 50775646 50775832 1 1 2 1 True 0 0 0 0 TN -chr20 51953819 51953820 0 0 0 1 False 0 0 0 1 FP -chr20 53204099 53204252 2 2 2 1 True 0 0 0 0 TN +chr20 50775646 50775832 0 0 1 1 True 0 0 0 0 TN +chr20 51953819 51953820 0 0 0 0 False 0 0 0 0 TN +chr20 53204099 53204252 0 1 2 0 False 0 1 2 0 FN chr20 55624808 55625652 6 6 6 0 False 6 6 6 0 FN chr20 55627638 55628305 7 7 4 0 False 7 7 4 0 FN -chr20 55944272 55945175 2 2 2 1 True 1 1 2 0 FN -chr20 56280541 56281913 4 4 5 1 True 4 4 2 1 FN,FP +chr20 55944272 55945175 2 2 1 1 True 1 1 2 0 FN +chr20 56280541 56281913 4 4 4 1 True 5 5 2 1 FN,FP chr20 57090868 57091166 1 1 2 0 False 1 1 2 0 FN chr20 57110450 57110593 2 2 1 0 False 2 2 1 0 FN chr20 57190256 57190428 0 0 3 1 True 0 0 0 0 TN -chr20 57350856 57350920 1 1 1 0 False 1 1 1 0 FN +chr20 57350856 57350920 1 1 0 0 False 1 1 0 0 TP chr20 57949001 57949346 1 1 4 1 True 0 0 4 1 FN,FP -chr20 59384366 59384743 3 3 2 0 False 3 3 2 0 FN -chr20 60314443 60314711 2 2 2 0 False 2 2 2 0 FN -chr20 60703005 60703087 2 2 2 1 True 3 3 0 0 TP -chr20 61100921 61102405 1 1 4 1 True 4 4 0 0 TP -chr20 61201822 61202242 2 2 4 1 True 1 1 0 0 TP -chr20 61282925 61283479 4 4 2 0 False 4 4 2 0 FN +chr20 59384366 59384743 2 2 2 0 False 2 2 2 0 FN +chr20 60314443 60314711 2 1 1 0 False 2 1 1 0 FN +chr20 60703005 60703087 2 2 1 1 True 3 3 0 0 TP +chr20 61100921 61102405 1 1 3 1 True 4 4 0 0 TP +chr20 61201822 61202242 1 2 4 1 True 1 1 0 0 TP +chr20 61282925 61283479 3 3 2 0 False 3 3 2 0 FN chr20 61289662 61290273 1 1 2 1 True 0 0 0 0 TN -chr20 61329345 61329441 0 0 0 2 False 0 0 0 2 FP -chr20 61562109 61562252 0 0 2 1 True 1 1 0 0 TP +chr20 61329345 61329441 0 0 0 1 False 0 0 0 1 FP +chr20 61562109 61562252 0 0 1 1 True 1 1 0 0 TP chr20 61744401 61744592 2 2 1 0 False 2 2 1 0 FN chr20 61783958 61784698 3 3 1 0 False 3 3 1 0 FN -chr20 62057602 62058768 1 1 3 1 True 1 1 0 0 TP +chr20 62057602 62058768 1 1 2 1 True 1 1 0 0 TP chr20 62270413 62270827 1 1 3 1 True 3 3 0 0 TP -chr20 62321396 62321730 2 2 3 0 False 2 2 3 0 FN -chr20 62349641 62349826 1 1 5 1 True 0 0 2 1 FN,FP -chr20 62360410 62360602 0 0 8 2 True 2 2 2 1 FN,FP +chr20 62321396 62321730 2 2 2 0 False 2 2 2 0 FN +chr20 62349641 62349826 1 1 4 1 True 0 0 2 1 FN,FP +chr20 62360410 62360602 0 0 6 2 True 1 1 1 1 FN,FP chr20 62830650 62830697 2 2 1 1 True 1 1 0 0 TP -chr20 62875241 62875404 2 2 3 0 False 2 2 3 0 FN +chr20 62875241 62875404 2 2 2 0 False 2 2 2 0 FN chr20 63028066 63029030 4 4 1 1 True 2 2 0 0 TP -chr20 63049093 63049159 3 3 1 0 False 3 3 1 0 FN +chr20 63049093 63049159 1 1 1 0 False 1 1 1 0 FN chr20 63154687 63154921 1 1 1 0 False 1 1 1 0 FN -chr20 63167473 63167564 2 2 1 0 False 2 2 1 0 FN -chr20 63221509 63221721 1 1 2 1 True 0 0 0 0 TN +chr20 63167473 63167564 2 2 0 0 False 2 2 0 0 TP +chr20 63221509 63221721 1 1 1 1 True 0 0 0 0 TN chr20 63372214 63372400 2 2 1 0 False 2 2 1 0 FN -chr20 63491957 63492390 1 1 3 1 True 2 2 1 0 FN +chr20 63491957 63492390 1 1 2 1 True 2 2 1 0 FN chr20 63535751 63536002 1 1 2 0 False 1 1 2 0 FN chr20 63559415 63559719 1 1 4 1 True 3 3 0 0 TP -chr20 63641847 63642015 1 1 2 1 True 0 0 0 0 TN -chr20 63693449 63693732 1 1 6 1 True 10 10 0 0 TP +chr20 63641847 63642015 0 0 1 0 False 0 0 1 0 FN +chr20 63693449 63693732 1 1 5 1 True 10 10 0 0 TP chr20 63770936 63771014 0 0 0 2 False 0 0 0 2 FP -chr20 63948594 63948653 2 2 1 1 True 0 0 0 1 FP +chr20 63948594 63948653 2 2 0 0 False 2 2 0 0 TP chr20 63964805 63966113 1 1 1 0 False 1 1 1 0 FN -chr20 64065882 64065883 0 0 0 1 False 0 0 0 1 FP +chr20 64065882 64065883 0 0 0 0 False 0 0 0 0 TN chr20 64090733 64091007 0 0 0 2 False 0 0 0 2 FP -chr20 64097039 64097040 0 0 0 2 False 0 0 0 2 FP +chr20 64097039 64097040 0 0 0 0 False 0 0 0 0 TN chr20 64125360 64127875 3 3 3 0 False 3 3 3 0 FN -chr20 64131913 64133856 5 5 8 1 True 5 5 6 5 FN,FP +chr20 64131913 64133856 4 5 8 1 True 5 5 6 5 FN,FP chr20 64134990 64136330 3 3 1 0 False 3 3 1 0 FN chr20 64173438 64176330 4 4 7 3 True 10 10 5 2 FN,FP diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json index c4e13143..739c8c21 100644 --- a/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json +++ b/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json @@ -1,11 +1,11 @@ { - "TP-base": 408, - "TP-comp": 408, - "FP": 35, - "FN": 108, - "precision": 0.9209932279909706, - "recall": 0.7906976744186046, - "f1": 0.8508863399374348, - "base cnt": 516, - "comp cnt": 443 + "TP-base": 422, + "TP-comp": 416, + "FP": 38, + "FN": 129, + "precision": 0.9162995594713657, + "recall": 0.7658802177858439, + "f1": 0.8343646923508332, + "base cnt": 551, + "comp cnt": 454 } \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt index fc8fd4c9..da659223 100644 --- a/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt +++ b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt @@ -24,7 +24,7 @@ chr20 18209097 18210727 3 3 2 1 True 5 5 0 0 TP chr20 18675650 18675915 2 2 0 0 False 2 2 0 0 TP chr20 19663366 19663526 2 2 0 0 False 2 2 0 0 TP chr20 20337200 20337707 1 1 6 2 True 3 3 0 0 TP -chr20 20354570 20358323 7 7 9 1 True 14 14 0 0 TP +chr20 20354570 20358323 7 7 9 1 True 16 16 0 0 TP chr20 20458640 20458937 2 2 0 0 False 2 2 0 0 TP chr20 21120212 21120539 2 2 1 0 True 1 1 0 0 TP chr20 21721174 21721735 2 2 1 0 True 3 3 0 0 TP @@ -73,7 +73,7 @@ chr20 58519902 58520372 2 2 0 0 False 2 2 0 0 TP chr20 58694862 58695411 2 2 0 0 False 2 2 0 0 TP chr20 59442036 59442273 2 2 0 0 False 2 2 0 0 TP chr20 60087391 60087965 2 2 0 0 False 2 2 0 0 TP -chr20 60314330 60315020 2 2 2 0 True 6 6 0 0 TP +chr20 60314330 60315020 2 2 2 0 True 5 5 0 0 TP chr20 60764031 60764634 2 2 0 0 False 2 2 0 0 TP chr20 61176725 61176974 2 2 0 0 False 2 2 0 0 TP chr20 61201683 61202474 2 2 4 1 True 7 7 0 0 TP @@ -85,7 +85,7 @@ chr20 61475406 61475726 2 2 0 0 False 2 2 0 0 TP chr20 61744188 61744654 2 2 1 0 True 2 2 0 0 TP chr20 61783403 61784839 3 3 1 0 True 4 4 0 0 TP chr20 61919676 61921374 2 2 0 0 False 2 2 0 0 TP -chr20 62057573 62059139 1 1 3 1 True 8 8 0 0 TP +chr20 62057573 62059139 1 1 3 1 True 7 7 0 0 TP chr20 62212844 62213874 4 4 0 0 False 4 4 0 0 TP chr20 62270279 62271094 1 1 3 1 True 4 4 0 0 TP chr20 62317837 62318459 2 2 0 0 False 2 2 0 0 TP diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ad2c051e81d70fcd18bbddaf87dc9140.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_06433b401328232c8c4a2f2278e2fb4c.msa similarity index 77% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_ad2c051e81d70fcd18bbddaf87dc9140.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_06433b401328232c8c4a2f2278e2fb4c.msa index 107a7831..ee0d8578 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ad2c051e81d70fcd18bbddaf87dc9140.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_06433b401328232c8c4a2f2278e2fb4c.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:56280441-56282014 +>syndip_1_chr20:56280441-56282013 aaaaaggtaacatccatatacagatataatatctataacatatatagatatatggatata acatccatatatagatatatctatatatctatctatagctac------------------ ----------------------------------------------atctacagatatct @@ -24,20 +24,20 @@ tagat--atatagatacatctatatagatatatagatatatagatacatctatatagata tattgatacat--atagatacatctatatagattagatatatatagatacatctatatag attagatatatatagatacatctatatagattagatatatatagatacatctatatatag atatatagatatatatagatacatctatatatagacatatagatatatatagatacatct -atatatagatatatagatgtatatagatacatctatat--atagatatatagatgtatat -agatacatctatatatagatatatagatgtatatagatacatctatatatagatatatag -atgtatatagatacatctatat--atagatatatagatgtatatagatacatctatatat -agatatatagatgtatatagatacatctatatatagatatatagatgtatatagatacat -ctatatatagatatatagatgtatatagatacatctatatatagatatatagatgtatat -agatacatctatatatagatatatagatgtatatagatacatagatatatatagatacat -ttatgtatatatatatgtatatatagatatatagatatatatagatacatctacacagag -agatatatagaaacatctacacagggagatatatagatacatctacatagagagatatat -agatacatctacatagagagatatatagatacatctacatagagagatatatagatacat -ctacatagagagatatatagatacatctacacagagagatatatagaaacatctacacag -ggagatatatagatacatctacacagagagatatatagatacatctacatagagagatat -atagatacatctacatagagagatatatagatacatctacatagagagatatatagatac -atctacatagagagatatatagatacatc ->syndip_2_chr20:56280441-56282014 +atatatagatatatagatgtatatagatacatctatatatagatatatagatgtatatag +atacatctatatatagatatatagatgtatatagatacatctatatatagatatatagat +gtatatagatacatctatatatagatatatagatgtatatagatacatctatatatagat +atatagatgtatatagatacatctatatatagatatatagatgtatatagatacatctat +atatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagat +acatctatatatagatatatagatgtatatagatacatagatatatatagatacatttat +gtatatatatatgtatatatagatatatagatatatatagatacatctacacagagagat +atatagaaacatctacacagggagatatatagatacatctacatagagagatatatagat +acatctacatagagagatatatagatacatctacatagagagatatatagatacatctac +atagagagatatatagatacatctacacagagagatatatagaaacatctacacagggag +atatatagatacatctacacagagagatatatagatacatctacatagagagatatatag +atacatctacatagagagatatatagatacatctacatagagagatatatagatacatct +acatagagagatatatagatacat +>syndip_2_chr20:56280441-56282013 aaaaaggtaacatccatatacagatataatatctataacatatatagatatatggatata acatccatatatagatatatctatatatctatctatagctacatctacagatatctatag ctacatctacagatatctacagatatctatagctacatctacagatatctacagatatct @@ -63,11 +63,11 @@ ttgatacatatagatacatctatatagatatatagatatatagatacatctata------ ------------------------------------------------------------ -------------------------------tagatatatatagatacatctatatatag acatatagatatatatagatacatctatatatagacatatagatatatatagatacatct -atatatagatatatagatatatatagatacatctacacagagagatatatagaaacatct -acacagggagatatatagatacatctacacagagagatatatagatacatctacatagag -agatatatagatacatctatatagagagatatatagatacatctacatagagagatatat -agatacatctacatagagagatatatagatacatctacatagagagatatatagatacat -c----------------------------------------------------------- +atatatagatatatagatatatatagatacatctacacagag------agatatatagaa +acatctacacagggagatatatagatacatctacacagagagatatatagatacatctac +atagagagatatatagatacatctatatagagagatatatagatacatctacatagagag +a--------tatatagatacatctacatagagaga--------tatatagatacatctac +atagagagatatatagatacat-------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -75,8 +75,8 @@ c----------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------ ->p:HG002_1_chr20:56280441-56282014 +------------------------ +>p:HG002_1_chr20:56280441-56282013 aaaaaggtaacatccatatacagatataatatctataacatatatagatatatggatata acatccatatatagatatatctatatatctatctatagctacatctacagatatctatag ctacatctacagatatctacagatatctatagctacatctacagatatctacagatatct @@ -102,10 +102,10 @@ ttgatacatatagatacatctatatagatatatagatatatagatacatctata------ ------------------------------------------------------------ -------------------------------tagatatatagatata----tagatacat ctatatagatatatatagatacatctatatatagacatatagatatatatagatacatct -atatatagatatatagatatatatagatacatctacacagagagatatatagaaacatct -acacagggagatatatagatacatctacacagagagatatatagatacatctacatagag -agatatatagatacatctacatagagagatatatagatacatctacatagagagatatat -agatacatctacatagagagatatatagatacatc------------------------- +atatatagatatatagatatatatagatacatctacacagag------agatatatagaa +acatctacacagggagatatatagatacatctacacagagagatatatagatacatctac +atagagagatatatagatacatctacatagagagatatatagatacatctacatagagag +a--------tatatagatacatctacatagagaga--------tatatagatacat---- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -114,8 +114,8 @@ agatacatctacatagagagatatatagatacatc------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------ ->p:HG002_2_chr20:56280441-56282014 +------------------------ +>p:HG002_2_chr20:56280441-56282013 aaaaaggtaacatccatatacagatataatatctataacatatatagatatatggatata acatccatatatagatatatctatatatctatctatagctac------------------ ----------------------------------------------atctacagatatct @@ -141,20 +141,20 @@ ttgatacatatagatacatctatatagatatatagatatatagatacatctatatagata tatagatatatagatacatacatctatatagattagatatatatagatacatctatatag attagatatatatagatacatctatatagattagatatatatagatacatctatatatag atatatagatatatatagatacatctatatatagatatatagatatatatagatacatct -atatatagatatatagatgtatatagatacatctatat--atagatatatagatgtatat -agatacatctatatatagatatatagatgtatatagatacatctatatatagatatatag -atgtatatagatacatctatat--atagatatatagatgtatatagatacatctatatat -agatatatagatgtatatagatacatctatatatagatatatagatgtatatagatacat -ctatatatagatatatagatgtatatagatacatctatatatagatatatagatgtatat -agatacatctatatatagatatatagatgtatatagatacatagatatatatagatacat -ttatgtatatatatatgtatatatagatatatagatatatatagatacatctacacagag -agatatatagaaacatctacacagggagatatatagatacatctacatagagagctatat -agatatatatagatacatctatatatagacatatagatatatatagatacatctatatat -agatatatagatatatatagatacatctacacagagagatatatagaaacatctacacag -ggagatatatagatacatctacacagagagatatatagatacatctacatagagagatat -atagatacatctacatagagagatatatagatacatctacatagagagatatatagatac -atctacatagagagatatatagatacatc ->ref_chr20:56280441-56282014 +atatatagatatatagatgtatatagatacatctatatatagatatatagatgtatatag +atacatctatatatagatatatagatgtatatagatacatctatatatagatatatagat +gtatatagatacatctatatatagatatatagatgtatatagatacatctatatatagat +atatagatgtatatagatacatctatatatagatatatagatgtatatagatacatctat +atatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagat +acatctatatatagatatatagatgtatatagatacatagatatatatagatacatttat +gtatatatatatgtatatatagatatatagatatatatagatacatctacacagagagat +atatagaaacatctacacagggagatatatagatacatctacatagagagctatatagat +atatatagatacatctatatatagacatatagatatatatagatacatctatatatagat +atatagatatatatagatacatctacacagagagatatatagaaacatctacacagggag +atatatagatacatctacacagagagatatatagatacatctacatagagagatatatag +atacatctacatagagagatatatagatacatctacatagagagatatatagatacatct +acatagagagatatatagatacat +>ref_chr20:56280441-56282013 aaaaaggtaacatccatatacagatataatatctataacatatatagatatatggatata acatccatatatagatatatctatatatctatctatagctac------------------ --------------atctacagatatctatagctacatctacagatatctacagatatct @@ -180,10 +180,10 @@ ttgatacatatagatacatctatatagatatatagatatatagatacatctata------ ------------------------------------------------------------ -------------------------------tagatatatagatata----tagatacat ctatatagatatatatagatacatctatatatagacatatagatatatatagatacatct -atatatagatatatagatatatatagatacatctacacagagagatatatagaaacatct -acacagggagatatatagatacatctacacagagagatatatagatacatctacatagag -agatatatagatacatctacatagagagatatatagatacatctacatagagagatatat -agatacatctacatagagagatatatagatacatc------------------------- +atatatagatatatagatatatatagatacatctacacagag------agatatatagaa +acatctacacagggagatatatagatacatctacacagagagatatatagatacatctac +atagagagatatatagatacatctacatagagagatatatagatacatctacatagagag +a--------tatatagatacatctacatagagaga--------tatatagatacat---- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -192,4 +192,4 @@ agatacatctacatagagagatatatagatacatc------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------ +------------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_36dc8f9607000ef7378ba372de940929.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_09e5224f3ed49d0a0d63118c15970e8f.msa similarity index 84% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_36dc8f9607000ef7378ba372de940929.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_09e5224f3ed49d0a0d63118c15970e8f.msa index 63bf4003..dd108ec0 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_36dc8f9607000ef7378ba372de940929.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_09e5224f3ed49d0a0d63118c15970e8f.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:50775546-50775933 +>syndip_1_chr20:50775546-50775932 tttctcattctgtctctccaaagatttccatatatatatatatatatatatatatatata tatatatatataaatataaatatattctatatattcatatatatatattctatatattca tatatataaatatattctatatattcatatataaatatattccatatatataaatatatt @@ -6,8 +6,8 @@ ccatatatt---tatatataaatatatatcatatatttatatataaatatatatcatata tttatatataaatatatatcatatatttatatat-aatatatatcatatatttatatata aatatatatcatatatttatatataaatatatatcatatatttatatataatatatatca tata-ttatatataaatatatatcatatatttatatataaatatatatcatatattaata -tatatcatatatttatatattaatatatatcatatatttatatatt ->syndip_2_chr20:50775546-50775933 +tatatcatatatttatatattaatatatatcatatatttatatat +>syndip_2_chr20:50775546-50775932 tttctcattctgtctctccaaagatttccatatatatatatatatatatatatatatata tatatatatataaatataaatatattctatatattcatatatatatattctatatattca tatatataaatatattctatatattcatatatataaatatattctatatattcatata-t @@ -15,8 +15,8 @@ aaatatattccatatatataaatatattccatatatttatatataaatatatatcatata tttatatataaatatatatcatatatttatatataaatatatatcatatatttatatat- aatatatatcatatatttatatataaatatatatcatatatttatatataatatatatca tata-ttatatataaatatatatcatatatttatatataaatatatatcatatattaata -tatatcatatatttatatattaatatatatcatatatttatatatt ->p:HG002_1_chr20:50775546-50775933 +tatatcatatatttatatattaatatatatcatatatttatatat +>p:HG002_1_chr20:50775546-50775932 tttctcattctgtctctccaaagatttccatatatatatatatatatatatatatatata tatatatatataaatataaatatattctatatattcatatatatatattctatatattca tatatataaatatattctatatattcatatataaatatatattctatatattcatata-t @@ -24,8 +24,8 @@ aaatatattccatatatataaatatattccatatatttatatataaatatatatcatatc catatatataaatatattccatatatttatatataaatatatatcatatatttatatata aatatatatcatatatttatatataaatatatatcatatatttatatataatatatatca tatatttatatataaatatatatcatatatttatatataaatatatatcatatattaata -tatatcatatatttatatattaatatatatcatatatttatatatt ->p:HG002_2_chr20:50775546-50775933 +tatatcatatatttatatattaatatatatcatatatttatatat +>p:HG002_2_chr20:50775546-50775932 tttctcattctgtctctccaaagatttccatatatatatatatatatatatatatatata tatatatatataaatataaatatattctatatattcatatatatatattctatatattca tatatataaatatattctatatattcatatataaatatattccatatatataaatatatt @@ -33,8 +33,8 @@ ccatatatt---tatatataaatatatatcatatatttatatataaatatatatcatata tttatatataaatatatatcatatatttatatat-aatatatatcatatatttatatata aatatatatcatatatttatatataaatatatatcatatatttatatataatatatatca tata-ttatatataaatatatatcatatatttatatataaatatatatcatatattaata -tatatcatatatttatatattaatatatatcatatatttatatatt ->ref_chr20:50775546-50775933 +tatatcatatatttatatattaatatatatcatatatttatatat +>ref_chr20:50775546-50775932 tttctcattctgtctctccaaagatttccatatatatatatatatatatatatatatata tatatatatataaatataaatatattctatatattcatatatatatattctatatattca tatatataaatatattctatatattcatatataaatatattccatatatataaatatatt @@ -42,4 +42,4 @@ ccatatatt---tatatataaatatatatcatatatttatatataaatatatatcatata tttatatataaatatatatcatatatttatatat-aatatatatcatatatttatatata aatatatatcatatatttatatataaatatatatcatatattaatatatatcatatat-- -----ttatatattaatatatatcatatatttatatat---------------------- ----------------------------------------------t +--------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c42f829bb3fad0eeedf846ea3be67cc8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0a842177b0a019f7a4fb813c41b08d1e.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_c42f829bb3fad0eeedf846ea3be67cc8.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_0a842177b0a019f7a4fb813c41b08d1e.msa index 8f675fc1..d4cd5f85 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c42f829bb3fad0eeedf846ea3be67cc8.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_0a842177b0a019f7a4fb813c41b08d1e.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63491857-63492491 +>syndip_1_chr20:63491857-63492490 gatggggaggtggatggatagatggatggatggatggatggatggatggatggatggggg gatagatggatggatggatggatggacggacggatggggagg--------tggatggatg gatggatggatggatggatggatggatgaggagatgaacggatggatgagatggatggat @@ -31,8 +31,8 @@ ggatggggaaatggatggatggaaggatggatggatagggaggtgggtggatggatggat ggatggatgtacagaaggatggatgggtggggaggtgggtgagtggatgaatggatggat ggatagatagaaggatggatgggtgggacaatagatggatggatagagagaaggatggat gggtggggagatagatggatggatggatggatggatggatagagagaaggatggatggtt -gagacaatggatggatggatggatggatggagagatggatggatggatggat ->syndip_2_chr20:63491857-63492491 +gagacaatggatggatggatggatggatggagagatggatggatggatgga +>syndip_2_chr20:63491857-63492490 gatggggaggtggatggatagatggatggatggatggatggatggatggatggatggggg gatagatggatggatggatggatggacggacggatggggaggtggatggatggatggatg gatggatggatggatggatggatggatgaggagatgaacggatggatgagatggatggat @@ -65,8 +65,8 @@ ggatggataaatggatggatggaaggatggatggataggtaggtgggtggatggatggat ggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggatggat ggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaaggatggat gggtggg----tagatggatggatggatggatggatggatagagagaaggatggatggtt -gagacaatggatggatggatggatggatggagagatggatggatggatggat ->p:HG002_1_chr20:63491857-63492491 +gagacaatggatggatggatggatggatggagagatggatggatggatgga +>p:HG002_1_chr20:63491857-63492490 gatggggaggtggatggatagatggatggatggatggatggatggatggatggatggggg gatagatggatggatggatggatggacggacggatggggaggtggatggatggatggatg gatggatggatggatggatggatggatgaggagatgaacggatggatgagatggatggat @@ -99,8 +99,8 @@ ggatggataaatggatggatggaaggatggatggataggtaggtgggtggatggatggat ggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggatggat ggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaaggatggat gggtggg----tagatggatggatggatggatggatggatagagagaaggatggatggtt -gagacaatggatggatggatggatggatggagagatggatggatggatggat ->p:HG002_2_chr20:63491857-63492491 +gagacaatggatggatggatggatggatggagagatggatggatggatgga +>p:HG002_2_chr20:63491857-63492490 gatggggaggtggatggatagatggatggatggatggatggatggatggatggatggggg gatagatggatggatggatggatggacggacggatggggaggtggatggatggatggatg gatggatggatggatggatggatggatgaggagatgaacggatggatgagatggatggat @@ -133,8 +133,8 @@ ggatggataaatggatggatggaaggatggatggataggtaggtgggtggatggatggat ggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggatggat ggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaaggatggat gggtggg----tagatggatggatggatggatggatggatagagagaaggatggatggtt -gagacaatggatggatggatggatggatggagagatggatggatggatggat ->ref_chr20:63491857-63492491 +gagacaatggatggatggatggatggatggagagatggatggatggatgga +>ref_chr20:63491857-63492490 gatggggaggtggatggatagatggatggatggatggatggatggatggatggatggggg gatagatggatggatggatggatggacggacggatggggaggtggatggatggatggatg gatggatggatggatggatggatggatgaggagatgaacggatggatgagatggatggat @@ -167,4 +167,4 @@ ggatggataaatggatggatggaaggatggatggataggtaggtgggtggatggatggat ggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggatggat ggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaaggatggat gggtggg----tagatggatggatggatggatggatggatagagagaaggatggatggtt -gagacaatggatggatggatggatggatggagagatggatggatggatggat +gagacaatggatggatggatggatggatggagagatggatggatggatgga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9be1536e40a58a7128ddc75d12940a3e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0c8572a4abbd43dfe7727d1bbe104e58.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_9be1536e40a58a7128ddc75d12940a3e.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_0c8572a4abbd43dfe7727d1bbe104e58.msa index 79c1ab78..68732c67 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9be1536e40a58a7128ddc75d12940a3e.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_0c8572a4abbd43dfe7727d1bbe104e58.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:16257641-16259446 +>syndip_1_chr20:16257641-16259445 ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat @@ -42,8 +42,8 @@ tccccatcccaaacacacacaca-------------------------ccttccccatcc caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg -gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag ->syndip_2_chr20:16257641-16259446 +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaa +>syndip_2_chr20:16257641-16259445 ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat @@ -87,8 +87,8 @@ tccccatcccaaacacacacacaccttcccatcccaaacacacacaccccttccccatcc caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg -gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag ->p:HG002_1_chr20:16257641-16259446 +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaa +>p:HG002_1_chr20:16257641-16259445 ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa gtctgtttctaagcagcagcctgatggatccatttttataatctgaaatcagatatcata cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat @@ -123,7 +123,7 @@ ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat -cccaaacacacacccattccccatcccagacacacccacccgttccccatcc-------- +cccaaacacacacccattccccatcccagacacacccacccgttccccatc--------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -132,8 +132,8 @@ cccaaacacacacccattccccatcccagacacacccacccgttccccatcc-------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------- ->p:HG002_2_chr20:16257641-16259446 +------------------------------------------------ +>p:HG002_2_chr20:16257641-16259445 ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat @@ -177,8 +177,8 @@ tccccatcccaaacacacacaca-------------------------ccttccccatcc caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg -gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag ->ref_chr20:16257641-16259446 +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaa +>ref_chr20:16257641-16259445 ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat @@ -222,4 +222,4 @@ tccccatcccaaacacacacaca-------------------------ccttccccatcc caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg -gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaag +gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2f584d342cd0122481374518f9e81904.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0d2e507e60453c89bd248c945dc7f54d.msa similarity index 93% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_2f584d342cd0122481374518f9e81904.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_0d2e507e60453c89bd248c945dc7f54d.msa index 2221e0dc..948c549e 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2f584d342cd0122481374518f9e81904.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_0d2e507e60453c89bd248c945dc7f54d.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:32722324-32723313 +>syndip_1_chr20:32722324-32723312 acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc @@ -15,8 +15,8 @@ ta-------aataataataataataataaagacttgtgatcctctccctctccctctccc tctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtc tccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgct gccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcc -tgcgattgcaggcacgcgccgccacgcctgactggtt ->syndip_2_chr20:32722324-32723313 +tgcgattgcaggcacgcgccgccacgcctgactggt +>syndip_2_chr20:32722324-32723312 acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc @@ -33,8 +33,8 @@ taaataaataataataataataataataaagacttgtgatcctctccctctccctctccc tctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtc tccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgct gccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcc -tgcgattgcaggcacgcgccgccacgcctgactggtt ->p:HG002_1_chr20:32722324-32723313 +tgcgattgcaggcacgcgccgccacgcctgactggt +>p:HG002_1_chr20:32722324-32723312 acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc @@ -51,8 +51,8 @@ ta-------aataataataataataataaagacttgtgatcctctccctctccctctccc tctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtc tccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgct gccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcc -tgcgattgcaggcacgcgccgccacgcctgactggtt ->p:HG002_2_chr20:32722324-32723313 +tgcgattgcaggcacgcgccgccacgcctgactggt +>p:HG002_2_chr20:32722324-32723312 acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc @@ -69,8 +69,8 @@ ta-------aataataataataataataaagacttgtgatcctctccctctccctctccc tctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtc tccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgct gccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcc -tgcgattgcaggcacgcgccgccacgcctgactggtt ->ref_chr20:32722324-32723313 +tgcgattgcaggcacgcgccgccacgcctgactggt +>ref_chr20:32722324-32723312 acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc @@ -87,4 +87,4 @@ ta-------aataataataataataataaagacttgtgatcctctccctctccctctccc tctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtc tccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgct gccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcc -tgcgattgcaggcacgcgccgccacgcctgactggtt +tgcgattgcaggcacgcgccgccacgcctgactggt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_be4bf563ccc78c76f28205e487e0c322.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0dd22c519e7416f2e879bd43c26d9682.msa similarity index 92% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_be4bf563ccc78c76f28205e487e0c322.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_0dd22c519e7416f2e879bd43c26d9682.msa index ed4a8e48..3d9e7894 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_be4bf563ccc78c76f28205e487e0c322.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_0dd22c519e7416f2e879bd43c26d9682.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:34235650-34236314 +>syndip_1_chr20:34235650-34236313 agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag @@ -11,8 +11,8 @@ ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat -cccagcactttgggaggccgaagcgggc ->syndip_2_chr20:34235650-34236314 +cccagcactttgggaggccgaagcggg +>syndip_2_chr20:34235650-34236313 agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag @@ -25,8 +25,8 @@ ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat -cccagcactttgggaggccgaagcgggc ->p:HG002_1_chr20:34235650-34236314 +cccagcactttgggaggccgaagcggg +>p:HG002_1_chr20:34235650-34236313 agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag @@ -39,8 +39,8 @@ ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat -cccagcactttgggaggccgaagcaggc ->p:HG002_2_chr20:34235650-34236314 +cccagcactttgggaggccgaagcagg +>p:HG002_2_chr20:34235650-34236313 agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag @@ -53,8 +53,8 @@ ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat -cccagcactttgggaggccgaagcaggc ->ref_chr20:34235650-34236314 +cccagcactttgggaggccgaagcagg +>ref_chr20:34235650-34236313 agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag @@ -67,4 +67,4 @@ ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggaaggagaaag--aa aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat -cccagcactttgggaggccgaagcgggc +cccagcactttgggaggccgaagcggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ae2bc435a754945d8db9c5a5fad60896.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_157340f8623d37786583821b8bd25147.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_ae2bc435a754945d8db9c5a5fad60896.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_157340f8623d37786583821b8bd25147.msa index dd71635f..fa589a59 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ae2bc435a754945d8db9c5a5fad60896.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_157340f8623d37786583821b8bd25147.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:61100821-61102506 +>syndip_1_chr20:61100821-61102505 ctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccac atctggagagacccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctg gagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggaga @@ -29,8 +29,8 @@ tcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctacttcct gtgtcacacctggagagaccccgagtgagggcagacggccacatcctctatttcctgtgt cacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcaca catggagagaccccgagtgagggcagaaggccacatcctctacttcctgtgtcacaccta -gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacct ->syndip_2_chr20:61100821-61102506 +gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacc +>syndip_2_chr20:61100821-61102505 ctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccac atctggagagacccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctg gagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggaga @@ -61,8 +61,8 @@ tcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctcttctacttcct gtgtcacacctggagaggccccgagtgagggcagacggccacctcctctacttcctgtgt cacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcaca catggagagaccctgagtgagggcagaaggccacatcctctacttcctgtgtcacaccta -gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacct ->p:HG002_1_chr20:61100821-61102506 +gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacc +>p:HG002_1_chr20:61100821-61102505 ctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccac atctggagagacccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctg gagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggaga @@ -93,8 +93,8 @@ tcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctacttcct gtgtcacacctggagagaccccgagtgagggcagacggccacatcctctatttcctgtgt cacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcaca catggagagaccccgagtgagggcagaaggccacatcctctacttcctgtgtcacaccta -gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacct ->p:HG002_2_chr20:61100821-61102506 +gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacc +>p:HG002_2_chr20:61100821-61102505 ctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccac atctggagagacccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctg gagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggaga @@ -125,8 +125,8 @@ tcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctacttcct gtgtcacacctggagagaccccgagtgagggcagacggccacatcctctatttcctgtgt cacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcaca catggagagaccccgagtgagggcagaaggccacatcctctacttcctgtgtcacaccta -gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacct ->ref_chr20:61100821-61102506 +gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacc +>ref_chr20:61100821-61102505 ctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccac atctggagagacccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctg gagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggaga @@ -157,4 +157,4 @@ tcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctacttcct gtgtcacacctggagagaccccgagtgagggcagacggccacatcctctatttcctgtgt cacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcaca catggagagaccccgagtgagggcagaaggccacatcctctacttcctgtgtcacaccta -gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacct +gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_34829e853039a0b83260fb740af39cda.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_1c44d23cb30292b3d1f847e04365e588.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_34829e853039a0b83260fb740af39cda.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_1c44d23cb30292b3d1f847e04365e588.msa index 5365dadd..a94a3423 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_34829e853039a0b83260fb740af39cda.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_1c44d23cb30292b3d1f847e04365e588.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:24407883-24409098 +>syndip_1_chr20:24407883-24409097 ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg ttggagccacaggaggtgatatagggtgcttccggccctggccatagggtacttctggga @@ -19,8 +19,8 @@ gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta -ctaaaagcacaaaaat ->syndip_2_chr20:24407883-24409098 +ctaaaagcacaaaaa +>syndip_2_chr20:24407883-24409097 ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg ttggagccacaggaggtgatatagggtgcttccagccctggccatagggtacttctggga @@ -41,8 +41,8 @@ gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta -ctaaaagcacaaaaat ->p:HG002_1_chr20:24407883-24409098 +ctaaaagcacaaaaa +>p:HG002_1_chr20:24407883-24409097 ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg ttggagccacaggaggtgatatagggtgcttccagccctggccatagggtacttctggga @@ -63,8 +63,8 @@ gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta -ctaaaagcacaaaaat ->p:HG002_2_chr20:24407883-24409098 +ctaaaagcacaaaaa +>p:HG002_2_chr20:24407883-24409097 ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg ttggagccacaggaggtgatatagggtgcttccggccctggccatagggtacttctggga @@ -85,8 +85,8 @@ gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta -ctaaaagcacaaaaat ->ref_chr20:24407883-24409098 +ctaaaagcacaaaaa +>ref_chr20:24407883-24409097 ctcagtttattcatctataaaacagatgtggcagtggtagtgccacaattcacagcccag ttccaccttcctcacaggctcgtgataaagctccatttcctacccttcctctcagttatg ttggagccacaggaggtgatatagggtgcttccagccctggccatagggtacttctggga @@ -107,4 +107,4 @@ gaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatagga tacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccttg gccatctcctctcctttaagatacctacacttgttctttcccacccacaactgtatcagt cagcttttactgaataacaaagcacccctaacctcagtgcatgatgaaaccctgtctcta -ctaaaagcacaaaaat +ctaaaagcacaaaaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_afe59e2c01695d7d2653b661248a80ef.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_1d20ababbd3c82b9d4be9155373214aa.msa similarity index 86% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_afe59e2c01695d7d2653b661248a80ef.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_1d20ababbd3c82b9d4be9155373214aa.msa index 7fd8c4ee..a0be7d9f 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_afe59e2c01695d7d2653b661248a80ef.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_1d20ababbd3c82b9d4be9155373214aa.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:23560783-23561292 +>syndip_1_chr20:23560783-23561291 taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca gcattcctttctctctctttctttctttctttctttctttccttccttccttccttcctt @@ -7,8 +7,8 @@ ccttccttccttccttccttccttccttcct----------------------------- ----------------------ttctttctttctttctttctttctttctttctttcttt ttttctttct-------ttctttctttctttttcttttacagagtcttactcttgttgcc caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca -ttcaagaaattctcctgcctcagcctccagagtagctgggat ->syndip_2_chr20:23560783-23561292 +ttcaagaaattctcctgcctcagcctccagagtagctggga +>syndip_2_chr20:23560783-23561291 taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca gcattcctttctctctctttctttctttctttctttctttctttctttctttctttcttt @@ -17,8 +17,8 @@ ctttccttctttccttctttccttctttccttctttccttctttccttctttccttcttt ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca -ttcaagaaattctcctgcctcagcctccagagtagctgggat ->p:HG002_1_chr20:23560783-23561292 +ttcaagaaattctcctgcctcagcctccagagtagctggga +>p:HG002_1_chr20:23560783-23561291 taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca gcattcctttctctctctttctttctttctttctttctttctttctttctttctttcttt @@ -27,8 +27,8 @@ ctttccttctttccttctttccttctttccttctttccttctttccttctttccttcttt ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc caggctgtagtgcagtggtgtgatctcggctgactgcaacctccacctctgcctcctgca -ttcaagaaattctcctgcctcagcctccagagtagctgggat ->p:HG002_2_chr20:23560783-23561292 +ttcaagaaattctcctgcctcagcctccagagtagctggga +>p:HG002_2_chr20:23560783-23561291 taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca gcattcctttctctctctttctttctttctttctttctttccttccttccttccttcctt @@ -37,8 +37,8 @@ ccttccttccttccttccttccttccttcct----------------------------- ----------------------ttctttctttctttctttctttctttctttctttcttt ttttctttct-------ttctttctttctttttcttttacagagtcttactcttgttgcc caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca -ttcaagaaattctcctgcctcagcctccagagtagctgggat ->ref_chr20:23560783-23561292 +ttcaagaaattctcctgcctcagcctccagagtagctggga +>ref_chr20:23560783-23561291 taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca gcattcctttctctttctttctttctttctttctttctttctttctttctttctttcctt @@ -47,4 +47,4 @@ ctttccttctttccttctttccttctttccttctttccttctttccttctttcc------ ------ttctttccttctttccttctttctttctttctttctttctttctttctttcttt ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca -ttcaagaaattctcctgcctcagcctccagagtagctgggat +ttcaagaaattctcctgcctcagcctccagagtagctggga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7051e6b8ca568da2ec784100ee158134.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_1d7c9e595e1b2ef479098d45351d36d3.msa similarity index 75% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_7051e6b8ca568da2ec784100ee158134.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_1d7c9e595e1b2ef479098d45351d36d3.msa index 98015e47..e2dd4670 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7051e6b8ca568da2ec784100ee158134.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_1d7c9e595e1b2ef479098d45351d36d3.msa @@ -1,44 +1,44 @@ ->syndip_1_chr20:63559315-63559820 +>syndip_1_chr20:63559315-63559819 gcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgt gagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgg gag--------------------ggagtcagggtcaggtgggaggagtcagggtcagatg ggagtcagtcagagtcaggtgggag-gagtcagggtcaggtgggaggagtcagggtcagg -tgggagg--------------------agtcagggtcaggtgggaggagtcagggtcaga +tgggag--------------------gagtcagggtcaggtgggaggagtcagggtcaga tgggagtcagtcagagtcaggtgggag-gagtcagggtcaggtggga------------- ----ggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcagg -tgggaggagtcagggtcaggtgggagg--------------------------------- ----------------------------- ->syndip_2_chr20:63559315-63559820 +tgggaggagtcagggtcaggtgggag---------------------------------- +--------------------------- +>syndip_2_chr20:63559315-63559819 gcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgt gagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgg gaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcagggtcaggtg ggag-gagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcagg -tgggagg----------------------------------------------------- +tgggag------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------- ->p:HG002_1_chr20:63559315-63559820 +--------------------------- +>p:HG002_1_chr20:63559315-63559819 gcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgt gagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgg gaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcagggtcaggtg ggag-gagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcagg -tgggagg----------------------------------------------------- +tgggag------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------- ->p:HG002_2_chr20:63559315-63559820 +--------------------------- +>p:HG002_2_chr20:63559315-63559819 gcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgt gagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgg gaggg--------------------agtcagggtcaggtgggaggagtcagggtcaggtg ggag-gagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcagg -tgggagg--------------------agtcagggtcaggt---cggagtcagggtcagg +tgggag--------------------gagtcagggtcaggt---cggagtcagggtcagg tgggag-gagtcagggtcaggtgggagtcagtcagggtcaggtggga------------- ----ggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcagg -tgggaggagtcagggtcaggtgggagg--------------------------------- ----------------------------- ->ref_chr20:63559315-63559820 +tgggaggagtcagggtcaggtgggag---------------------------------- +--------------------------- +>ref_chr20:63559315-63559819 gcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgt gagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgg gaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcagggtcaggtg @@ -47,4 +47,4 @@ tgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaga tgggagtcagtcagagtcaggtgggag-gagtcagggtcaggtgggaggagtcagggtca ggtcggagtcagggtcaggtgggaggagtcagggtcaggtgggagtcagtcagggtcagg tgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcag -gtgggaggagtcagggtcaggtgggagg +gtgggaggagtcagggtcaggtgggag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_94d9fc221f90d8b60251faa405fdfde1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_20bd20e862e124e808d69a4270d4895a.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_94d9fc221f90d8b60251faa405fdfde1.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_20bd20e862e124e808d69a4270d4895a.msa index 38be0070..3b13513e 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_94d9fc221f90d8b60251faa405fdfde1.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_20bd20e862e124e808d69a4270d4895a.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:5041757-5042810 +>syndip_1_chr20:5041757-5042809 cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat @@ -19,8 +19,8 @@ gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg -ttctgttttttttctttttctcttgccttctatgctttccatt ->syndip_2_chr20:5041757-5042810 +ttctgttttttttctttttctcttgccttctatgctttccat +>syndip_2_chr20:5041757-5042809 cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat @@ -41,8 +41,8 @@ gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg -ttctgttttttttctttttctcttgccttctatgctttccatt ->p:HG002_1_chr20:5041757-5042810 +ttctgttttttttctttttctcttgccttctatgctttccat +>p:HG002_1_chr20:5041757-5042809 cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta gcgggatttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat @@ -63,8 +63,8 @@ gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt gatctgctcgtcttggcctcccaaagtgttgggattataggcatgagccaccacaaccga cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg -ttctgttttttttctttttctcttgccttctatgctttccatt ->p:HG002_2_chr20:5041757-5042810 +ttctgttttttttctttttctcttgccttctatgctttccat +>p:HG002_2_chr20:5041757-5042809 cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat @@ -85,8 +85,8 @@ gactcccaaagtgctgggattacaggtgtgagccaccgtgcccggcctaattttgtattt ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcccgatctcaggt gatccgctcgtcttggcctcccaaagtgttgggattacaggcatgagccaccacacccag cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg -ttctgttttttttctttttctcttgccttctatgctttccatt ->ref_chr20:5041757-5042810 +ttctgttttttttctttttctcttgccttctatgctttccat +>ref_chr20:5041757-5042809 cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat @@ -107,4 +107,4 @@ gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg -ttctgttttttttctttttctcttgccttctatgctttccatt +ttctgttttttttctttttctcttgccttctatgctttccat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f949c02c5b00935cf4bd4b3c660a5ded.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2404771658108744496a59df4a81aa48.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_f949c02c5b00935cf4bd4b3c660a5ded.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_2404771658108744496a59df4a81aa48.msa index 88b78cdc..10546aa5 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f949c02c5b00935cf4bd4b3c660a5ded.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_2404771658108744496a59df4a81aa48.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:20337185-20337725 +>syndip_1_chr20:20337185-20337724 tggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatgcatgg atggatggatggatggacagaatgggtgggtggatggatggatggatggatggatggatg gatagatgggtgggtggatggatggatggatagatgggtggatggatagatgggtggatg @@ -32,8 +32,8 @@ gatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatg gatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtg gatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtg ggtggatggatggatggatagatgggtgggtgggtggatggatggatggatggatagaat -aaaaaagaaagctaggacatggttctagtgttcttagcagacg ->syndip_2_chr20:20337185-20337725 +aaaaaagaaagctaggacatggttctagtgttcttagcagac +>syndip_2_chr20:20337185-20337724 tggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatgcatgg atggatggatggatggacagaatgggtgggtggatggatggatggatggatggatggatg gatggatagatgggtgggtggatggatggatggatagatgggtggatggataaatggatg @@ -67,8 +67,8 @@ gatggatagatgggtgggtgggtggatggatggatggatggataga-------------- ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------------------------------at -aaaaaagaaagctaggacatggttctagtgttcttagcagacg ->p:HG002_1_chr20:20337185-20337725 +aaaaaagaaagctaggacatggttctagtgttcttagcagac +>p:HG002_1_chr20:20337185-20337724 tggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatgcatgg atggatggatggatggacagaatgggtgggtggatggatggatggatagatggatggatg gatggatggatggatggatggatggatggatggatagatgggtgggtgggtggatggatg @@ -102,8 +102,8 @@ gatggatagatgggtgggtgggtggatggatggatggatggataga-------------- ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------------------------------at -aaaaaagaaagctaggacatggttctagtgttcttagcagacg ->p:HG002_2_chr20:20337185-20337725 +aaaaaagaaagctaggacatggttctagtgttcttagcagac +>p:HG002_2_chr20:20337185-20337724 tggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatgcatgg atggatggatggatggacagaatgggtgggtggatggatggatggatggatggatggatg gatagatgggtgggtggatggatggatggatagatgggtggatggatagatgggtggatg @@ -137,8 +137,8 @@ gatggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggata aatggatggatggatggatggatagatgggtgggtggatggatggatggatggatggatg gatggatggatagatagatgggtgggtggatggatggatggatagatgggtgggtgggtg gatggatggatggatggatagatgggtgggtgggtggatggatggatggatggatagaat -aaaaaagaaagctaggacatggttctagtgttcttagcagacg ->ref_chr20:20337185-20337725 +aaaaaagaaagctaggacatggttctagtgttcttagcagac +>ref_chr20:20337185-20337724 tggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatgcatgg atggatggatggatggacagaatgggtgggtggatggatggatggatagatggatggatg gatggatggatggatggatggatggatggatggatagatgggtgggtgggtggatggatg @@ -172,4 +172,4 @@ gatagatgggtgggtgggtggatggatggatggatggataga------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------------------------------at -aaaaaagaaagctaggacatggttctagtgttcttagcagacg +aaaaaagaaagctaggacatggttctagtgttcttagcagac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_717cdf145eb3b53da7ad74d00c183277.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_241ebaea2bd4d12cce6bff185f492856.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_717cdf145eb3b53da7ad74d00c183277.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_241ebaea2bd4d12cce6bff185f492856.msa index be26405d..683e67f5 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_717cdf145eb3b53da7ad74d00c183277.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_241ebaea2bd4d12cce6bff185f492856.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:22082166-22084006 +>syndip_1_chr20:22082166-22084005 tatgtatatataatatatgtatatactatacatgtatatattatattatacatgtatata ttataagtatatactatacatgcatgtattatatgtatatactatacatgcatgtattat atgtatatattatacatgcatgtattatatgtatatattatacatgcatgtattatatgt @@ -36,8 +36,8 @@ gccttaaactctaaggtcttctgtgcattcattcctgcttcctattacatatatattata tagatacatatataatatatacatatatactacataatatatgcatatataatatataca tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatat ->syndip_2_chr20:22082166-22084006 +tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataata +>syndip_2_chr20:22082166-22084005 tatgtatatataatatatgtatatactatacatgtatatattatattatacatgtatata ttataagtatatactatacatgcatgtattatatgtatatac------------------ ----------tatacatgcatgtattatatgtatatattatacatgcatgtattatatgt @@ -74,9 +74,9 @@ atatattatatatacgtatatattaatatacatatatatgtgtctcattataccaataat gccttaaactctaaggtcttctgtgcattcattcctgcttcctattacatatatattata tagatacatatataatatatacatatatactacataatatatgcatatataatatataca tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataatat----------------------------------- -------------------------------------------------------- ->p:HG002_1_chr20:22082166-22084006 +tatgttgtatatgtatatataata------------------------------------ +------------------------------------------------------ +>p:HG002_1_chr20:22082166-22084005 tatgtatatataatatatgtatatactatacatgtatatattatattatacatgtatata ttataagtatatactatacatgcatgtattatatgtatatac------------------ ----------tatacatgcatgtattatatgtatatattatacatgcatgtattatatgt @@ -113,9 +113,9 @@ atatattatatatacgtatatattaatatacatatatatgtgtctcattataccaataat gccttaaactctaaggtcttctgtgcattcattcctgcttcctattacatatatattata tagatacatatataatatatacatatatactacataatatatgcatatataatatataca tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataatat----------------------------------- -------------------------------------------------------- ->p:HG002_2_chr20:22082166-22084006 +tatgttgtatatgtatatataata------------------------------------ +------------------------------------------------------ +>p:HG002_2_chr20:22082166-22084005 tatgtatatataatatatgtatatactatacatgtatatattatattatacatgtatata ttataagtatatactatacatgcatgtattatatgtatatactatacatgcatgtattat atgtatatattatacatgcatgtattatatgtatatattatacatgcatgtattatatgt @@ -153,8 +153,8 @@ gccttaaactctaaggtcttctgtgcattcattcctgcttcctattacatatatattata tagatacatatataatatatacatatatactacataatatatgcatatataatatataca tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatat ->ref_chr20:22082166-22084006 +tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataata +>ref_chr20:22082166-22084005 tatgtatatataatatatgtatatactatacatgtatatattatattatacatgtatata ttataagtatatactatacatgcatgtattatatgtatatactatacatgcatgtattat atgtatatattatacatgcatgtattatatgtatatattatacatgcatgtattatatgt @@ -191,5 +191,5 @@ atatattatatatacgtatatattaatatacatatatatgtgtctcattataccaataat gccttaaactctaaggtcttctgtgcattcattcctgcttcctattacatatatattata tagatacatatataatatatacatatatactacataatatatgcatatataatatataca tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataatat----------------------------------- -------------------------------------------------------- +tatgttgtatatgtatatataata------------------------------------ +------------------------------------------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e19b79eecb589d0faff3fd8eba62aeef.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_24fd8ff0eec7e23320c9f4385933e3f5.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_e19b79eecb589d0faff3fd8eba62aeef.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_24fd8ff0eec7e23320c9f4385933e3f5.msa index 65babcd3..b3b44011 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e19b79eecb589d0faff3fd8eba62aeef.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_24fd8ff0eec7e23320c9f4385933e3f5.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:55627244-55628551 +>syndip_1_chr20:55627244-55628550 gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt @@ -21,8 +21,8 @@ tgtatacattatatattatgtatacatatatgtata------------------------ tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat -atttggttat ->syndip_2_chr20:55627244-55628551 +atttggtta +>syndip_2_chr20:55627244-55628550 gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt @@ -45,8 +45,8 @@ tacgtatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat -atttggttat ->p:HG002_1_chr20:55627244-55628551 +atttggtta +>p:HG002_1_chr20:55627244-55628550 gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt @@ -69,8 +69,8 @@ tacgtatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat -atttggttat ->p:HG002_2_chr20:55627244-55628551 +atttggtta +>p:HG002_2_chr20:55627244-55628550 gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt @@ -93,8 +93,8 @@ tgtatacattatatattatgtatacatatatgtata------------------------ tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata cataggagagagtcactgccctgagtcttaaatgtaacccttattaaagaaaatatttta gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat -atttggttat ->ref_chr20:55627244-55628551 +atttggtta +>ref_chr20:55627244-55628550 gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt @@ -117,4 +117,4 @@ tacatatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat -atttggttat +atttggtta diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c35059068940421b229c17e87e720ab8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_29711408027d779b5a2977378e72a9e5.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_c35059068940421b229c17e87e720ab8.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_29711408027d779b5a2977378e72a9e5.msa index 0c0de308..605e7ec2 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c35059068940421b229c17e87e720ab8.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_29711408027d779b5a2977378e72a9e5.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:61783303-61784940 +>syndip_1_chr20:61783303-61784939 ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat @@ -26,8 +26,8 @@ aggagaatgtaag----------------------------------------------- cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc -ctccttcctggcctccag ->syndip_2_chr20:61783303-61784940 +ctccttcctggcctcca +>syndip_2_chr20:61783303-61784939 ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat @@ -55,8 +55,8 @@ a----------------------------------------------------------- cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc -ctccttcctggcctccag ->p:HG002_1_chr20:61783303-61784940 +ctccttcctggcctcca +>p:HG002_1_chr20:61783303-61784939 ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat @@ -84,8 +84,8 @@ a----------------------------------------------------------- cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc -ctccttcctggcctccag ->p:HG002_2_chr20:61783303-61784940 +ctccttcctggcctcca +>p:HG002_2_chr20:61783303-61784939 ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat @@ -113,8 +113,8 @@ aggagaatgtaag----------------------------------------------- cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc -ctccttcctggcctccag ->ref_chr20:61783303-61784940 +ctccttcctggcctcca +>ref_chr20:61783303-61784939 ctccaaaggcacattctatatgatttttgcccacaacctttccttaatatgtacatgttt tctagataaaaacattaaatacagctaaagtgacatcaaggtctccctcccttcctttcc tccaatacgtgagagaaatgtaatcccagttccttgggacagttctcgaggccctcagat @@ -142,4 +142,4 @@ ccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctccgatatcctgtg cccccaggagaatgtaagcccagttcctcggaacagttctccaggccctcagatgtcctg tgcccccggggcctcatcagacattaagcatgcagtccctttgcagctctggatggcgcg agtttcccacgtcccatccccttcctggctatgggcaagtgcaggctggatcctggcctc -ctccttcctggcctccag +ctccttcctggcctcca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9b6ec2bc5fb37634cbfbb07c76684bcf.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2acb877c85cd2b044d5bd5f0537d9b2e.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_9b6ec2bc5fb37634cbfbb07c76684bcf.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_2acb877c85cd2b044d5bd5f0537d9b2e.msa index 62de31e0..a58724da 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9b6ec2bc5fb37634cbfbb07c76684bcf.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_2acb877c85cd2b044d5bd5f0537d9b2e.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:38123699-38124104 +>syndip_1_chr20:38123699-38124103 taataataatatataatatttataataataatatatataatatgtatatataatatacat atacctattatatataatatacctattatatataatatacatatacctattatatataat atacctattatatataagatacctattatatataatatacatatacctattatatatata @@ -19,8 +19,8 @@ attatatattatatataatacacattatatattatatataatacacattatatattatat aatacacattatatattatatataatacacattatatatataatacacattatatattat atataatacataatacacattatatattatatataatacacattatatataatatataac acacattatatataatatataacacacattatatattatatataatacacattatatatt -atata ->syndip_2_chr20:38123699-38124104 +atat +>syndip_2_chr20:38123699-38124103 taataataatatataatatttataataataatatatataatatgtatatataatatacat atacctattatatataatatacctattatatataatatacatatacctattatatataat atacctattatatataagatacctattatatataatatacatatacctattatatatata @@ -41,8 +41,8 @@ attatatattatatataatacacattatatattatatataatacacattatatattatat aatacacattatatattatatataatacacattatatatataatacacattatatattat atataatacataatacacattatatattatatataatacacattatatataatatataac acacattatatataatatataacacacattatatattatatataatacacattatatatt -atata ->p:HG002_1_chr20:38123699-38124104 +atat +>p:HG002_1_chr20:38123699-38124103 taataataatatataatatttataataataatatatataatatgtatatataatatacat atacctattatatataatatacctattatatataatatacataaacctattatatataat atacctattatatataagatacctattatatataatatacctatacctattatatatata @@ -63,8 +63,8 @@ attatatattatatataatacacattatatattatatataatacacattatatattatat aatacacattatatattatatataatacacattatatatataatacacattatatattat atataatacataatacacattatatattatatataatacacattatatataatatataac acacattatatataatatataacacacattatatattatatataatacacattatatatt -atata ->p:HG002_2_chr20:38123699-38124104 +atat +>p:HG002_2_chr20:38123699-38124103 taataataatatataatatttataataataatatatataatatgtatatataatatacat atacctattatatataatatacctattatatataatatacataaacctattatatataat atacctattatatataagatacctattatatataatatacctatacctattatatatata @@ -85,8 +85,8 @@ attatatattatatataatacacattatatattatatataatacacattatatattatat aatacacattatatattatatataatacacattatatatataatacacattatatattat atataatacataatacacattacctattatatataatacacattatatataatatataac acacattatatataatatataacacacattatatattatatataatacacattatatatt -atata ->ref_chr20:38123699-38124104 +atat +>ref_chr20:38123699-38124103 taataataatatataatatttataataataatatatataatatgtatatataatatacat atacctattatatataatatacctattatatataatatacataaacctattatatataat atacctattatatataagatacctattatatataatatacctat--------tatatata @@ -95,7 +95,7 @@ atataatatacctattatatatatataatatacctattatatatataatatacctattat atatataatatacctattatatatataatatacctattatatataa-----------tac acattatatataata----tataacaca---------------------------catta tatataata----tataacacacattatatattata----tataatacacattatatatt -atata------------------------------------------------------- +atat-------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -107,4 +107,4 @@ atata------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------ +---- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_141ad6632a3577b19e9a4616ecdf6bbe.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2b01ba4d781cd0dddb30db4277c8ca9b.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_141ad6632a3577b19e9a4616ecdf6bbe.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_2b01ba4d781cd0dddb30db4277c8ca9b.msa index ed52f700..4bc15bf6 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_141ad6632a3577b19e9a4616ecdf6bbe.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_2b01ba4d781cd0dddb30db4277c8ca9b.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:55624382-55625908 +>syndip_1_chr20:55624382-55625907 atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat @@ -35,8 +35,8 @@ tatagtatactatatactatactatactatagtatactctatagtatataaagacatata tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg -aaggtcaccttcatcc ->syndip_2_chr20:55624382-55625908 +aaggtcaccttcatc +>syndip_2_chr20:55624382-55625907 atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat @@ -73,8 +73,8 @@ tatagtatactatatactatactatactatagtatactctatagtatataaagacatata tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg -aaggtcaccttcatcc ->p:HG002_1_chr20:55624382-55625908 +aaggtcaccttcatc +>p:HG002_1_chr20:55624382-55625907 atcccagctacttgggaggctgaggcaggataatcacttcaatcagtgaggtggaggctg cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat @@ -111,8 +111,8 @@ tatagtatactatatactatactatactatagtatactctatagtatataaagacatata tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg -aaggtcaccttcatcc ->p:HG002_2_chr20:55624382-55625908 +aaggtcaccttcatc +>p:HG002_2_chr20:55624382-55625907 atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat @@ -149,8 +149,8 @@ tatagtatactatatactatactatactatagtatactctatagtatataaagacatata tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg -aaggtcaccttcatcc ->ref_chr20:55624382-55625908 +aaggtcaccttcatc +>ref_chr20:55624382-55625907 atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat @@ -187,4 +187,4 @@ tatagtatactatatactatactatactatagtatactctatagtatataaagacatata tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg -aaggtcaccttcatcc +aaggtcaccttcatc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e0a1b90b66779bb5b8c7086145d6f100.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2bcd8e5fdfaa68491615ae8e8a2e7e21.msa similarity index 83% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_e0a1b90b66779bb5b8c7086145d6f100.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_2bcd8e5fdfaa68491615ae8e8a2e7e21.msa index e9579aa1..27c9e329 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e0a1b90b66779bb5b8c7086145d6f100.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_2bcd8e5fdfaa68491615ae8e8a2e7e21.msa @@ -1,40 +1,40 @@ ->syndip_1_chr20:17081116-17081511 +>syndip_1_chr20:17081116-17081510 tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca tgtggaattttattttattttattttattttattttattttattttattttattttattt tatt-------------------------------------------------------- ----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca -cctcagcctcccaagtagctgggactacaagtacgt ->syndip_2_chr20:17081116-17081511 +cctcagcctcccaagtagctgggactacaagtacg +>syndip_2_chr20:17081116-17081510 tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca tgtgga-----attttattttattttattttattttattttattttattttattttattt tatt-------------------------------------------------------- ----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca -cctcagcctcccaagtagctgggactacaagtacgt ->p:HG002_1_chr20:17081116-17081511 +cctcagcctcccaagtagctgggactacaagtacg +>p:HG002_1_chr20:17081116-17081510 tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca tgtgga-----attttattttattttattttattttattttattttattttattttattt tatt-------------------------------------------------------- ----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca -cctcagcctcccaagtagctgggactacaagtacgt ->p:HG002_2_chr20:17081116-17081511 +cctcagcctcccaagtagctgggactacaagtacg +>p:HG002_2_chr20:17081116-17081510 tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca tgtggaattttattttattttattttattttattttattttattttattttattttattt tatt-------------------------------------------------------- ----------ttattttattttattacgacaaggtctggctctgtcgcctaggctggagt gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca -cctcagcctcccaagtagctgggactacaagtacgt ->ref_chr20:17081116-17081511 +cctcagcctcccaagtagctgggactacaagtacg +>ref_chr20:17081116-17081510 tgaatattcttttatgtagtaaaagtataaaactatggctggtaaaaatgcatgccacat tgtggatcatgactacctctgggtcagaaggaaatgtgatgggtaaaggaatcaactcca tgtggaattttattttattttattttattttattttattttattttattttattttattt tattattttattttattttattttattttattttattttattttattttattttatttta ttttattttattattttattttattacgacaaggtctggctctgtcgcctaggctggagt gcattgtggtaatcttggcttactgcaacctctgcctcccagactcaaccagtcctccca -cctcagcctcccaagtagctgggactacaagtacgt +cctcagcctcccaagtagctgggactacaagtacg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_dd8b054c3bcd4f4a22fdac0fc01760de.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2c05a87978c7b4aa656e86b640a18690.msa similarity index 88% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_dd8b054c3bcd4f4a22fdac0fc01760de.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_2c05a87978c7b4aa656e86b640a18690.msa index f35203e4..6bac5dcb 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_dd8b054c3bcd4f4a22fdac0fc01760de.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_2c05a87978c7b4aa656e86b640a18690.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63027897-63028267 +>syndip_1_chr20:63027897-63028266 acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagagggccggtg @@ -10,8 +10,8 @@ agggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggga gggggccggcggggaggggccggtggggaggggccggtggggtggggccggtggggaggg ggccggtgggggggggcctgcagggagggggccggtggggaggaggctggtgaagtagcg tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca -gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc ->syndip_2_chr20:63027897-63028267 +gcttcatcaggttctcaattagcggagggcgctggcggtggaggaggg +>syndip_2_chr20:63027897-63028266 acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg @@ -23,8 +23,8 @@ ag-----------------------------ggggccggtggggagggggccggcgggga gggggccggcggggaggggccggtggggagtggtctg----------------------- -------------------gtggggagggggccggtggggaggaggctggtgaagtagcg tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca -gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc ->p:HG002_1_chr20:63027897-63028267 +gcttcatcaggttctcaattagcggagggcgctggcggtggaggaggg +>p:HG002_1_chr20:63027897-63028266 acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg @@ -36,8 +36,8 @@ ag-----------------------------ggggccggtggggagggggccggcgggga gggggccggcggggaggggccggtggggagtggtctg----------------------- -------------------gtggggagggggccggtggggaggaggctggtgaagtagcg tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca -gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc ->p:HG002_2_chr20:63027897-63028267 +gcttcatcaggttctcaattagcggagggcgctggcggtggaggaggg +>p:HG002_2_chr20:63027897-63028266 acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagagggccggtg @@ -49,8 +49,8 @@ agggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggga gggggccggcggggaggggccggtggggaggggccggtggggtggggccggtggggaggg ggccggtgggggggggcctgcagggagggggccggtggggaggaggctggtgaagtagcg tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca -gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc ->ref_chr20:63027897-63028267 +gcttcatcaggttctcaattagcggagggcgctggcggtggaggaggg +>ref_chr20:63027897-63028266 acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg @@ -62,4 +62,4 @@ gggag--------------tggttt----------------------------------- ------------------------------------------------------------ ---------------------------------ggtggggaggaggctggtgaagtagcg tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca -gcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc +gcttcatcaggttctcaattagcggagggcgctggcggtggaggaggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0b1f7552f96468523661603cd4269fe6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2e395a6e1327c3cee2e68d6b7c844cc7.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_0b1f7552f96468523661603cd4269fe6.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_2e395a6e1327c3cee2e68d6b7c844cc7.msa index 23695bd4..13fdbb64 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0b1f7552f96468523661603cd4269fe6.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_2e395a6e1327c3cee2e68d6b7c844cc7.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:5039849-5040600 +>syndip_1_chr20:5039849-5040599 agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat @@ -16,8 +16,8 @@ gggcaacatagggagaacttgtctctattt------------------------------ ------------------------------------------------------------ --------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca -acccggattagcctttt ->syndip_2_chr20:5039849-5040600 +acccggattagccttt +>syndip_2_chr20:5039849-5040599 agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat @@ -35,8 +35,8 @@ gggcaacatagggagaacttgtctctattt------------------------------ ------------------------------------------------------------ --------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca -acccggattagcctttt ->p:HG002_1_chr20:5039849-5040600 +acccggattagccttt +>p:HG002_1_chr20:5039849-5040599 agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat @@ -54,8 +54,8 @@ cgcggtggcgggcgcctaggcaggagaatggcgtgaacccgggaagcggagcttgcagtg agccgagattgcgccactgcagtccgcagtccgacctgggcgacagagagagactccgtc tcaaaaaaaaaaaaaaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca -acccggattagcctttt ->p:HG002_2_chr20:5039849-5040600 +acccggattagccttt +>p:HG002_2_chr20:5039849-5040599 agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat @@ -73,8 +73,8 @@ cgcggtggcgggcgcctaggcaggagaatggcgtgaacccgggaagcggagcttgcagtg agccgagattgcgccactgcagtccgcagtccgacctgggcgacagagagagactccgtc tc---aaaaaaaaaaaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca -acccggattagcctttt ->ref_chr20:5039849-5040600 +acccggattagccttt +>ref_chr20:5039849-5040599 agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat @@ -92,4 +92,4 @@ gggcaacatagggagaacttgtctctattt------------------------------ ------------------------------------------------------------ --------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca -acccggattagcctttt +acccggattagccttt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a9fdcb29d10f9c256c49525ef4fab80f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_32f6f2dff38622b1e9f06443baeb622f.msa similarity index 88% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_a9fdcb29d10f9c256c49525ef4fab80f.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_32f6f2dff38622b1e9f06443baeb622f.msa index a1bc1c22..d5ef8898 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a9fdcb29d10f9c256c49525ef4fab80f.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_32f6f2dff38622b1e9f06443baeb622f.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:62270313-62270928 +>syndip_1_chr20:62270313-62270927 ctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgt ccctccctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctcc ttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc @@ -9,8 +9,8 @@ ttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtc cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctct ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtcc ctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctc -tggcctctctgggtcct ->syndip_2_chr20:62270313-62270928 +tggcctctctgggtcc +>syndip_2_chr20:62270313-62270927 ctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgt ccctccctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctcc ttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc @@ -19,10 +19,10 @@ ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctga- ------------------------------------------cctctctgggtcctctcc ttgtccctctctgggtcctctccttgtc-------------------------------- ---------cctctctgggtcctctccttgtccctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct---------- +ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcc----------- ------------------------------------------------------------ ------------------ ->p:HG002_1_chr20:62270313-62270928 +---------------- +>p:HG002_1_chr20:62270313-62270927 ctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgt ccctccctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctcc ttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc @@ -31,10 +31,10 @@ ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctgg- ------------------------------------------cctctctgggtcctctc- ----------------------------------------ctctgggtcctctccttgtc cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct---------- +ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcc----------- ------------------------------------------------------------ ------------------ ->p:HG002_2_chr20:62270313-62270928 +---------------- +>p:HG002_2_chr20:62270313-62270927 ctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgt ccctccctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctcc ttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc @@ -45,8 +45,8 @@ ttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtc cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctct ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtcc ctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctc -tggcctctctgggtcct ->ref_chr20:62270313-62270928 +tggcctctctgggtcc +>ref_chr20:62270313-62270927 ctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgt ccctccctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctcc ttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc @@ -57,4 +57,4 @@ ttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtc cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctct ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtcc ctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctc -tggcctctctgggtcct +tggcctctctgggtcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6147414e8642b5c9ece9fffa3cd6290f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3309323b7a8f49f7d21f616b3f162df2.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_6147414e8642b5c9ece9fffa3cd6290f.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_3309323b7a8f49f7d21f616b3f162df2.msa index 85418d0f..d02c4b68 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6147414e8642b5c9ece9fffa3cd6290f.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_3309323b7a8f49f7d21f616b3f162df2.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:64134783-64136487 +>syndip_1_chr20:64134783-64136486 agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca @@ -27,8 +27,8 @@ tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc cctcagttttgtgtg---------------------------------tcacaaacacac acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta -gccgttattgagggacatcgaggtt ->syndip_2_chr20:64134783-64136487 +gccgttattgagggacatcgaggt +>syndip_2_chr20:64134783-64136486 agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca @@ -57,8 +57,8 @@ tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta -gccgttattgagggacatcgaggtt ->p:HG002_1_chr20:64134783-64136487 +gccgttattgagggacatcgaggt +>p:HG002_1_chr20:64134783-64136486 agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc cggtgtgtgatgttccccttgaaaaggaagcgtttctgcttctcctctttccggtccttg acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca @@ -87,8 +87,8 @@ tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta -gccgttattgagggacatcgaggtt ->p:HG002_2_chr20:64134783-64136487 +gccgttattgagggacatcgaggt +>p:HG002_2_chr20:64134783-64136486 agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc cggtgtgtgatgttccccttgaaaaggaagcgtttctgcttctcctctttccggtccttg acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca @@ -117,8 +117,8 @@ tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc cctcagttttgtgtg---------------------------------tcacaaacacac acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta -gccgttattgagggacatcgaggtt ->ref_chr20:64134783-64136487 +gccgttattgagggacatcgaggt +>ref_chr20:64134783-64136486 agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca @@ -147,4 +147,4 @@ tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta -gccgttattgagggacatcgaggtt +gccgttattgagggacatcgaggt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_02b73a4f2fb9c7243d2ae74002dc5b27.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_351515eae575f51a5c58a89edbda4b09.msa similarity index 92% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_02b73a4f2fb9c7243d2ae74002dc5b27.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_351515eae575f51a5c58a89edbda4b09.msa index b67a5751..9e58793b 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_02b73a4f2fb9c7243d2ae74002dc5b27.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_351515eae575f51a5c58a89edbda4b09.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:16395049-16395522 +>syndip_1_chr20:16395049-16395521 acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag @@ -8,8 +8,8 @@ gaggggaggccaagggaggggaggggaggagaggggaggccaagggaggggaggggaggg gaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggagaa gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg -gtattcaaa ->syndip_2_chr20:16395049-16395522 +gtattcaa +>syndip_2_chr20:16395049-16395521 acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtccaggcagaaa ggagatgaggaaggggagaggaggggagaggaggggag---------------------- @@ -19,8 +19,8 @@ ggagatgaggaaggggagaggaggggagaggaggggag---------------------- -----------------------gggaggggaggggagaggaggggaggccaagggagaa gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg -gtattcaaa ->p:HG002_1_chr20:16395049-16395522 +gtattcaa +>p:HG002_1_chr20:16395049-16395521 acagtcatggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcattggt gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtccaggcagaaa ggagatgaggaaggggagaggaggggagaggaggggag---------------------- @@ -30,8 +30,8 @@ ggagatgaggaaggggagaggaggggagaggaggggag---------------------- -----------------------gggaggggaggggagaggaggggaggccaagggagaa gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg -gtattcaaa ->p:HG002_2_chr20:16395049-16395522 +gtattcaa +>p:HG002_2_chr20:16395049-16395521 acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag @@ -41,8 +41,8 @@ gaggggaggccaagggaggggaggggaggagaggggaggccaagggaggggaggggaggg gaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggagaa gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg -gtattcaaa ->ref_chr20:16395049-16395522 +gtattcaa +>ref_chr20:16395049-16395521 acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag @@ -52,4 +52,4 @@ gaggggaggccaa----------------------------------------------- -----------------------gggaggggaggggaggagaggggaggccaagggagaa gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg -gtattcaaa +gtattcaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bd2f885276994e61366fc4ae806bc3c9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_35335f6151c790b9a47a9350279b1936.msa similarity index 93% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_bd2f885276994e61366fc4ae806bc3c9.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_35335f6151c790b9a47a9350279b1936.msa index 4e63868f..5194c214 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_bd2f885276994e61366fc4ae806bc3c9.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_35335f6151c790b9a47a9350279b1936.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:20295914-20296431 +>syndip_1_chr20:20295914-20296430 cagaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacc aacgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttcttt tcttcctccctcccttcct---tcccttccttcccttccttccctccttttcttccttct @@ -13,8 +13,8 @@ ccttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttc cttcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatc ccttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgc ttccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttcct -tctttctttcttttctttcttcctccc ->syndip_2_chr20:20295914-20296431 +tctttctttcttttctttcttcctcc +>syndip_2_chr20:20295914-20296430 cagaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacc aacgcctgcatgcttccctccttccttccttccttccctcc-ttccttccttccttcctt ccttcctgcctgcctgcctgccttcctgccttcccttcctccctccc--tccctacctcc @@ -29,8 +29,8 @@ ccttcctttcttcacccctcccccttccctcatcccttccctccttcccttccttccttc cttccctccttccttccct---tccttccttccttccctccttccttcccttccttcctt gcttccttccttccttcccttccttccttgcttccttccttccttcccttccttccttgc ttccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttcct -tctttctttcttttctttcttcctccc ->p:HG002_1_chr20:20295914-20296431 +tctttctttcttttctttcttcctcc +>p:HG002_1_chr20:20295914-20296430 cagaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacc aacgcctgcatgcttccctccttccttccttccttccctcc-ttccttccttccttcctt ccttcctgcctgcctgcctgccttcctgccttcccttcctccctccc--tccctacctcc @@ -45,8 +45,8 @@ ccttcctttcttcacccctcccccttccctcatcccttccctccttcccttccttccttc cttccctccttccttccct---tccttccttccttccctccttccttcccttccttcctt gcttccttccttccttcccttccttccttgcttccttccttccttcccttccttccttgc ttccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttcct -tctttctttcttttctttcttcctccc ->p:HG002_2_chr20:20295914-20296431 +tctttctttcttttctttcttcctcc +>p:HG002_2_chr20:20295914-20296430 cagaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacc aacgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttcttt tcttcctccctcccttcct---tcccttccttcccttccttccctccttttcttccttct @@ -61,8 +61,8 @@ ccttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttc cttcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatc ccttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgc ttccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttcct -tctttctttcttttctttcttcctccc ->ref_chr20:20295914-20296431 +tctttctttcttttctttcttcctcc +>ref_chr20:20295914-20296430 cagaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacc aacgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttcttt tcttcctccctcccttcct---tcccttccttc--------------------------- @@ -77,4 +77,4 @@ ccttcctttcttcacccctcccccttccctcatcccttccctccttcccttccttccttc cttccctccttccttccct----------------------------------------- ---------------------------------------------tccttccttccttgc ttccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttcct -tctttctttcttttctttcttcctccc +tctttctttcttttctttcttcctcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b6f4c42dfe3dd25d3029d99aa8472281.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_373e1d1ae04c109544621b85b6e2768d.msa similarity index 93% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_b6f4c42dfe3dd25d3029d99aa8472281.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_373e1d1ae04c109544621b85b6e2768d.msa index 070e9101..ed703593 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b6f4c42dfe3dd25d3029d99aa8472281.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_373e1d1ae04c109544621b85b6e2768d.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:62320931-62321974 +>syndip_1_chr20:62320931-62321973 aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga @@ -18,8 +18,8 @@ gccagcagaggggtggggccagt-----------------ggaggggtggggccagcgga ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag -gtcgacgttaacactggggtcaccaggctgtgtgggacttggat ->syndip_2_chr20:62320931-62321974 +gtcgacgttaacactggggtcaccaggctgtgtgggacttgga +>syndip_2_chr20:62320931-62321973 aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga @@ -39,8 +39,8 @@ gccagcagaggggtggggccagtggaggggtggggccagcggaggggtggggccagcgga ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag -gtcgacgttaacactggggtcaccaggctgtgtgggacttggat ->p:HG002_1_chr20:62320931-62321974 +gtcgacgttaacactggggtcaccaggctgtgtgggacttgga +>p:HG002_1_chr20:62320931-62321973 aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga @@ -60,8 +60,8 @@ gccagcagaggggtggggccagtggaggggtggggccagcggaggggtggggccagcgga ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag -gtcgacgttaacactggggtcaccaggctgtgtgggacttggat ->p:HG002_2_chr20:62320931-62321974 +gtcgacgttaacactggggtcaccaggctgtgtgggacttgga +>p:HG002_2_chr20:62320931-62321973 aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga @@ -81,8 +81,8 @@ gccagcagaggggtggggccagt-----------------ggaggggtggggccagcgga ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag -gtcgacgttaacactggggtcaccaggctgtgtgggacttggat ->ref_chr20:62320931-62321974 +gtcgacgttaacactggggtcaccaggctgtgtgggacttgga +>ref_chr20:62320931-62321973 aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga @@ -102,4 +102,4 @@ gccagcagaggggtggggtcagt-----------------ggaggggtggggccagtgga ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag -gtcgacgttaacactggggtcaccaggctgtgtgggacttggat +gtcgacgttaacactggggtcaccaggctgtgtgggacttgga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_376415b15834e0e44f2cec357e45842b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_376415b15834e0e44f2cec357e45842b.msa deleted file mode 100644 index f0fd442d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_376415b15834e0e44f2cec357e45842b.msa +++ /dev/null @@ -1,295 +0,0 @@ ->syndip_1_chr20:62057473-62059240 -tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag -atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga -cacaaagggcc------------------------------------------------- ------------------------------------------------------------- ----------------------------------------cagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggct -cggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggcca -cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct -acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaa -gacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggg -ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa -tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc -aggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacc -tcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggc -tcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggcc -acagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggc -ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaag -gacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagca -agacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggcctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacagtggggctcggggggccaa -cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg -gctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc -cacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacagg -cctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagga -aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag -caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg -ggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg -gacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga -cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc -aacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatg -gggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccag -gccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacag -gtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagg -aaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcggggggccaacctctccagtccccaaacacagtc -cccaacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccc -tcacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaag -ctgggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaagg -caggcctggagaagagcctgggaccaccgcggactgacc ->syndip_2_chr20:62057473-62059240 -tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag -atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga -cacaaagggcc------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------cagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctc----------------------------------------------------- ------------------------------------------------------------- ------------------------------------gggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaagga---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -cggacacaggtctacacaccaggccacagacaatggggctc------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------gggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc -aggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacc -tcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggc -tc---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------gggggccaacctctccagtccccaaacacagtc -cccaacagacaacttctcctgtcctcacatgcggctcccaacaaacaatttctcctgccc -tcacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaag -ctgggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaagg -caggcctggagaagagcctgggaccaccgcggactgacc ->p:HG002_1_chr20:62057473-62059240 -tccaagatccatgtaccccaacaccaccctacctggccacgctcctctcacaactttgag -atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga -cacaaagggcc------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------cagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctc----------------------------------------------------- ------------------------------------------------------------- ------------------------------------gggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaagga---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -cggacacaggtctacacaccaggccacagacaatggggctc------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------gggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc -aggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacc -tcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggc -tc---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------gggggccaacctctccagtccccaaacacagtc -cccaacagacaacttctcctgtcctcacatgcggctcccaacaaacaatttctcctgccc -tcacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaag -ctgggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaagg -caggcctggagaagagcctgggaccaccgcggactgacc ->p:HG002_2_chr20:62057473-62059240 -tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag -atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga -cacaaagggcc------------------------------------------------- ------------------------------------------------------------- ----------------------------------------cagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggct -cggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggcca -cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct -acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaa -gacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggg -ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa -tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc -aggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacc -tcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggc -tcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggcc -acagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggc -ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaag -gacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagca -agacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggcctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacagtggggctcggggggccaa -cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg -gctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc -cacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacagg -cctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagga -aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag -caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg -ggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg -gacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga -cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc -aacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatg -gggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccag -gccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacag -gtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagg -aaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcggggggccaacctctccagtccccaaacacagtc -cccaacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccc -tcacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaag -ctgggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaagg -caggcctggagaagagcctgggaccaccgcggactgacc ->ref_chr20:62057473-62059240 -tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag -atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga -cacaaagggcccagcaagacctcaggaaggacggacacaggcctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacacc -aggccacagacaatggggctc--------------------------------------- ------------------------------------gggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaagga---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -cggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaa -gacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggg -ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa -tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc -aggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacc -tcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggc -tcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggcc -acagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggc -ctacacaccaggccacagacaatggggctc------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------gggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcggggggccaacctctccagtccccaaacacagtc -cccaacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccc -tcacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaag -ctgggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaagg -caggcctggagaagagcctgggaccaccgcggactgacc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d27af66810a53f2070224212487e9431.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_37addba43ca0bef896cc3f8296ac4789.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_d27af66810a53f2070224212487e9431.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_37addba43ca0bef896cc3f8296ac4789.msa index 3c5fc164..9d06ac16 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d27af66810a53f2070224212487e9431.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_37addba43ca0bef896cc3f8296ac4789.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:64131704-64134056 +>syndip_1_chr20:64131704-64134055 aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc tcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagag @@ -66,8 +66,8 @@ tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc tcatgtcctatagagaccccctcactgtccactctcatggcctgtagagaccccctcact gtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcattt gctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaagggc -cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggccc ->syndip_2_chr20:64131704-64134056 +cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggcc +>syndip_2_chr20:64131704-64134055 aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc tcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagag @@ -135,8 +135,8 @@ tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc tcgtgtcctatagagaccccctcactgtccacccatatggcctgtagagaccccctcact gtccaccctcatggcctgtagagaccccctcactgtccaccctcaggaccctctgcattt gctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaagggc -cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggccc ->p:HG002_1_chr20:64131704-64134056 +cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggcc +>p:HG002_1_chr20:64131704-64134055 aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc tcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagag @@ -204,8 +204,8 @@ tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc tcgtgtcctatagagaccccctcactgtccacccatatggcctgtagagaccccctcact gtccaccctcatggcctgtagagaccccctcactgtccaccctcaggaccctctgcattt gctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaagggc -cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggccc ->p:HG002_2_chr20:64131704-64134056 +cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggcc +>p:HG002_2_chr20:64131704-64134055 aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc tcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagag @@ -273,8 +273,8 @@ tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc tcatgtcctatagagaccccctcactgtccactctcatggcctgtagagaccccctcact gtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcattt gctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaagggc -cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggccc ->ref_chr20:64131704-64134056 +cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggcc +>ref_chr20:64131704-64134055 aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc tcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagag @@ -342,4 +342,4 @@ tgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccc tcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcact gtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcattt gctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaagggc -cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggccc +cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_19907622767ec08f4f2a547410d2ecfb.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_37dc1e3da979ee027d03cd84019b4904.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_19907622767ec08f4f2a547410d2ecfb.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_37dc1e3da979ee027d03cd84019b4904.msa index 446dd9db..ec43eebc 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_19907622767ec08f4f2a547410d2ecfb.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_37dc1e3da979ee027d03cd84019b4904.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:13848064-13848750 +>syndip_1_chr20:13848064-13848749 tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag @@ -12,8 +12,8 @@ aagaagaggaagaggaagaggaagaggaagaagaagaagaagaagaagaagaagaagaag aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca -gagaatc ->syndip_2_chr20:13848064-13848750 +gagaat +>syndip_2_chr20:13848064-13848749 tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag @@ -27,8 +27,8 @@ aagaagaggaagaggaagaggaagag---------------gaagaagaagaagaagaag aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca -gagaatc ->p:HG002_1_chr20:13848064-13848750 +gagaat +>p:HG002_1_chr20:13848064-13848749 tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag @@ -42,8 +42,8 @@ aagaagaggaagaggaagaggaagag---------------gaagaagaagaagaagaag aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca -gagaatc ->p:HG002_2_chr20:13848064-13848750 +gagaat +>p:HG002_2_chr20:13848064-13848749 tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag @@ -57,8 +57,8 @@ aagaagaggaagaggaagaggaagaggaagaagaagaagaagaagaagaagaagaagaag aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca -gagaatc ->ref_chr20:13848064-13848750 +gagaat +>ref_chr20:13848064-13848749 tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg cgtctcaaaaaaaaaaaagaagaagaaaagtagaagacgaagatgaagaagaataagaag @@ -72,4 +72,4 @@ aaggagaaggagaaggagaaggagaagga------------------------------- aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaaata caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca -gagaatc +gagaat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_392581e26c6c6574757f793b72e768f0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3a3d4bda444ca93397f3574b58e71451.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_392581e26c6c6574757f793b72e768f0.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_3a3d4bda444ca93397f3574b58e71451.msa index f270ff15..681ffc5d 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_392581e26c6c6574757f793b72e768f0.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_3a3d4bda444ca93397f3574b58e71451.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:57090572-57091512 +>syndip_1_chr20:57090572-57091511 agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc @@ -17,8 +17,8 @@ acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct -ctttacctcaacaaggag ->syndip_2_chr20:57090572-57091512 +ctttacctcaacaagga +>syndip_2_chr20:57090572-57091511 agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc @@ -37,8 +37,8 @@ acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct -ctttacctcaacaaggag ->p:HG002_1_chr20:57090572-57091512 +ctttacctcaacaagga +>p:HG002_1_chr20:57090572-57091511 agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc @@ -57,8 +57,8 @@ acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct -ctttacctcaacaaggag ->p:HG002_2_chr20:57090572-57091512 +ctttacctcaacaagga +>p:HG002_2_chr20:57090572-57091511 agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt aagccacgaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc @@ -77,8 +77,8 @@ acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg attactgggtcctgccggtctggccaggcctggtcacaggccgggtcccagtcagcagct -ctttacctcaacaaggag ->ref_chr20:57090572-57091512 +ctttacctcaacaagga +>ref_chr20:57090572-57091511 agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc @@ -97,4 +97,4 @@ acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct -ctttacctcaacaaggag +ctttacctcaacaagga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3a73de403e528810fa08a7607a17d7f5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3a73de403e528810fa08a7607a17d7f5.msa deleted file mode 100644 index 2453346e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3a73de403e528810fa08a7607a17d7f5.msa +++ /dev/null @@ -1,115 +0,0 @@ ->syndip_1_chr20:53203999-53204353 -aatatctccttcatttttataatatgatactattatatcataattttataatatactatt -atatcatattatatgatactatttatatcatcatatgatgatatactat--tatatcatc -atatgatgatata--ctattatatcatcatatgatgatatg--atactatatcatcatat -gatgatatgatactatatcatcatatgatgat---atactatatcatcatatgatgatat -gatatactatatcatcatatgatgatatgatactatatcatcat-----atgatgatatg -atactatatcatcat-----atgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacat -gatgatatgatactatatcatcacatgatgatatgatactatatcatcacatgatgatat -gatactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatactat -atcatcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcat ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------ataacatgatgatatgatactatatcatcata -taacatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatca -tataacatgatgat---------------------------------------------- ------------------------------------------------------------- ------------------- ->syndip_2_chr20:53203999-53204353 -aatatctccttcatttttataatatgatactattatatcataattttataatatactatt -atatcatattatatgatactatttatatcatcatatgatgatatgatat--tatatcatc -atatgatgatatg--atactatatcatcatatgatgatatgatatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -g--atactatatcatcatatgatgatatgatactatatcatcat-----atgatgatatg -atactatatcatcat-----atgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcataacatgatgatatgatactatatcata -acatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcata -taacatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatca -tataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatcat -catataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatc -atcatataacatgatgat ->p:HG002_1_chr20:53203999-53204353 -aatatctccttcatttttataatatgatactattatatcataattttataatatactatt -atatcatattatatgatactatttatatcatcatatgatgatatgatatactatatcatc -atatgatgatatgatatactatatcatcatatgatgatatg--atactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -g--atactatatcatcatatgatgatatgatactatatcatcat-----atgatgatatg -atactatatcatcat-----atgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcataacatgatgatatgatactatatcata -acatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcata -taacatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatca -tataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatcat -catataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatc -atcatataacatgatgat ->p:HG002_2_chr20:53203999-53204353 -aatatctccttcatttttataatatgatactattatatcataattttataatatactatt -atatcatattatatgatactatttatatcatcatatgatgatatgatatactatatcatc -atatgatgatatg----attatatcatcatatgatgatatg--atactatatcatcatat -gatgatatgatactatatcatcatatgatgat---atactatatcatcatatgatgatat -g--atactatatcatcatatgatgatatgatactatatcatcat-----atgatgatatg -atactatatcatcat-----atgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacat -gatgatatgatactatatcatcacatgatgatatgatactatatcatcacatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------ataacatgatgatatgatactatatcatcata -taacatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatca -tataacatgatgat---------------------------------------------- ------------------------------------------------------------- ------------------- ->ref_chr20:53203999-53204353 -aatatctccttcatttttataatatgatactattatatcataattttataatatactatt -atatcatattatatgatactatttatatcatcatatgatgatatgatatactatatcatc -atatgatgatatgatatactatatcatcatatgatgatatg--atactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -g--atactatatcatcatatgatgatatgatactatatcatcatataacatgatgatatg -atactatatcatcatataacatgatgatatgatactatatcatcatataacatgatgat- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_946b797ceaa32d6c1b711e085ad7903e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3ba0420a0f6db81c0d76f7ba53ba5226.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_946b797ceaa32d6c1b711e085ad7903e.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_3ba0420a0f6db81c0d76f7ba53ba5226.msa index eac01e91..b000d0b7 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_946b797ceaa32d6c1b711e085ad7903e.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_3ba0420a0f6db81c0d76f7ba53ba5226.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:59383704-59385336 +>syndip_1_chr20:59383704-59385335 ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg @@ -33,8 +33,8 @@ gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc -ccatgaaataactttgctccccagattctgagcatgggt ->syndip_2_chr20:59383704-59385336 +ccatgaaataactttgctccccagattctgagcatggg +>syndip_2_chr20:59383704-59385335 ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg @@ -69,8 +69,8 @@ gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc -ccatgaaataactttgctccccagattctgagcatgggt ->p:HG002_1_chr20:59383704-59385336 +ccatgaaataactttgctccccagattctgagcatggg +>p:HG002_1_chr20:59383704-59385335 ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg @@ -105,8 +105,8 @@ gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc -ccatgaaataactttgctccccagattctgagcatgggt ->p:HG002_2_chr20:59383704-59385336 +ccatgaaataactttgctccccagattctgagcatggg +>p:HG002_2_chr20:59383704-59385335 ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg @@ -141,8 +141,8 @@ gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc -ccatgaaataactttgctccccagattctgagcatgggt ->ref_chr20:59383704-59385336 +ccatgaaataactttgctccccagattctgagcatggg +>ref_chr20:59383704-59385335 ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg @@ -177,4 +177,4 @@ gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg aggtgagaggggaggagctgagtggggaaggaggtaatgaggacaaggtgaggggaaagg aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc -ccatgaaataactttgctccccagattctgagcatgggt +ccatgaaataactttgctccccagattctgagcatggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4dff1cfc21c902e0e7568be207ccbd40.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3d73cc7182161a9c5e90b812c17b9c4a.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_4dff1cfc21c902e0e7568be207ccbd40.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_3d73cc7182161a9c5e90b812c17b9c4a.msa index 46a6aa62..55858c55 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4dff1cfc21c902e0e7568be207ccbd40.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_3d73cc7182161a9c5e90b812c17b9c4a.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:278800-279287 +>syndip_1_chr20:278800-279286 gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- ------------------------------------------------------------ @@ -17,8 +17,8 @@ gggagggagggcgggacggagggtgggagggagggagggatggaggga----gggaggga gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc -ggttgagcttgctgaggaagttctcacggc ->syndip_2_chr20:278800-279287 +ggttgagcttgctgaggaagttctcacgg +>syndip_2_chr20:278800-279286 gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa tgcgtcttccaggtggaggaagcaccacgtgcagtgggcggggaaaggcaggagagggcg cgcgagtgcgcggagggagggcgggacggagggagggagggcgggacggagggagggagg @@ -37,8 +37,8 @@ gggagggagggcgggagggatggagggagggagggcgggacggagggagggcgggaggga gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc -ggttgagcttgctgaggaagttctcacggc ->p:HG002_1_chr20:278800-279287 +ggttgagcttgctgaggaagttctcacgg +>p:HG002_1_chr20:278800-279286 gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa tgcgtcttccaggtggaggaagcaccacgtgcagtgggcggggaaaggcaggagagggcg cgcgagtgcgcggagggagggcgggacggagggagggagggcgggacggagggagggagg @@ -57,8 +57,8 @@ gggagggagggcgggagggatggagggagggagggcgggacggagggagggcgggaggga gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc -ggttgagcttgctgaggaagttctcacggc ->p:HG002_2_chr20:278800-279287 +ggttgagcttgctgaggaagttctcacgg +>p:HG002_2_chr20:278800-279286 gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- ------------------------------------------------------------ @@ -77,8 +77,8 @@ gggagggagggcgggacggagggtgggagggagggagggatggaggga----gggaggga gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc -ggttgagcttgctgaggaagttctcacggc ->ref_chr20:278800-279287 +ggttgagcttgctgaggaagttctcacgg +>ref_chr20:278800-279286 gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- ------------------------------------------------------------ @@ -97,4 +97,4 @@ gcgggagggcgggacggag----------------------------------------- gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga gggacggagggcgggcggatgccgcgggtctcaccgccagggtgtcctgctgctgcagca gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc -ggttgagcttgctgaggaagttctcacggc +ggttgagcttgctgaggaagttctcacgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3570b2394a58b5622e26496d8c6f1a42.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3f90779dcd8c05402fb060d819c516f1.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_3570b2394a58b5622e26496d8c6f1a42.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_3f90779dcd8c05402fb060d819c516f1.msa index d9ca2b8d..4170dc40 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3570b2394a58b5622e26496d8c6f1a42.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_3f90779dcd8c05402fb060d819c516f1.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:4032257-4033329 +>syndip_1_chr20:4032257-4033328 cccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgg gatatgaggagcccctctgcctggctgcccagtctggaaagt------------------ ----------------------gaggagcgtctctgcccggccgccatcccatctaggaa @@ -24,8 +24,8 @@ gcctctgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgcccc gtccgggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggg gggtcagccccctttccggcc--gccgcctgtccgggaggtgaggggcgcctctgcctgg ccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggag -gtgggggg ->syndip_2_chr20:4032257-4033329 +gtggggg +>syndip_2_chr20:4032257-4033328 cccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgg gatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccg gccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaa @@ -51,8 +51,8 @@ gcctctgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgcccc gtccgggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggg gggtcagccccctttccggcc--gccgcctgtccgggaggtgaggggcgcctctgcctgg ccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggag -gtgggggg ->p:HG002_1_chr20:4032257-4033329 +gtggggg +>p:HG002_1_chr20:4032257-4033328 cccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgg gatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccg gccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaa @@ -78,8 +78,8 @@ gcctctgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgcccc gtccgggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggg gggtcagccccccttccggccgggccgcctgtccgggaggtgaggggcgcctctgcctgg ccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggag -gtgggggg ->p:HG002_2_chr20:4032257-4033329 +gtggggg +>p:HG002_2_chr20:4032257-4033328 cccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgg gatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccg gccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaa @@ -105,8 +105,8 @@ gcctctgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgcccc gtccgggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggg gggtcagccccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctgg ccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggag -gtgggggg ->ref_chr20:4032257-4033329 +gtggggg +>ref_chr20:4032257-4033328 cccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgg gatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccg gccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaa @@ -129,7 +129,7 @@ ccagccgccccgtccgggaggggggagggggggtcagccccctgcccggccagccgcccc gtccgggagggaggt-ggggggggggtcagccccctttccggcc-gccg----------- ---------------------------------------cctgtccgggaggtgaggggc gcctctgcctggccgcccctactgggaagtgagga-cccctctgcccggccagccgcccc -gtccgggagggaggtgggggg--------------------------------------- +gtccgggagggaggtggggg---------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ --------- +------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5c074fb37f70d5e11502be5c009c13e2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_405fa3f356dead7f68ddb49001c0e603.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_5c074fb37f70d5e11502be5c009c13e2.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_405fa3f356dead7f68ddb49001c0e603.msa index 053f59de..22915bfb 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5c074fb37f70d5e11502be5c009c13e2.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_405fa3f356dead7f68ddb49001c0e603.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:20295855-20296666 +>syndip_1_chr20:20295855-20296665 gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt @@ -18,8 +18,8 @@ tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca -gatagtcaaataactgtaag ->syndip_2_chr20:20295855-20296666 +gatagtcaaataactgtaa +>syndip_2_chr20:20295855-20296665 gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca acgcctgcatgcttccctccttccttccttccttccttcctt-ccttccttccttccttc @@ -39,8 +39,8 @@ tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca -gatagtcaaataactgtaag ->p:HG002_1_chr20:20295855-20296666 +gatagtcaaataactgtaa +>p:HG002_1_chr20:20295855-20296665 gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca acgcctgcatgcttccctccttccttccttccttccttcctt-ccttccttccttccttc @@ -60,8 +60,8 @@ tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaaactgca -gatagtcaaataactgtaag ->p:HG002_2_chr20:20295855-20296666 +gatagtcaaataactgtaa +>p:HG002_2_chr20:20295855-20296665 gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt @@ -81,8 +81,8 @@ tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca -gatagtcaaataactgtaag ->ref_chr20:20295855-20296666 +gatagtcaaataactgtaa +>ref_chr20:20295855-20296665 gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt @@ -102,4 +102,4 @@ tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca -gatagtcaaataactgtaag +gatagtcaaataactgtaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8d91e35548435d3392527d244ebe8371.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4248c4ccdcf22249a1ca92c0fca9a551.msa similarity index 98% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_8d91e35548435d3392527d244ebe8371.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_4248c4ccdcf22249a1ca92c0fca9a551.msa index 3696203d..999ea0d2 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8d91e35548435d3392527d244ebe8371.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_4248c4ccdcf22249a1ca92c0fca9a551.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63491489-63493165 +>syndip_1_chr20:63491489-63493164 gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg @@ -49,8 +49,8 @@ agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat -cttgtacacgtcctgcagcggc ->syndip_2_chr20:63491489-63493165 +cttgtacacgtcctgcagcgg +>syndip_2_chr20:63491489-63493164 gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg @@ -101,8 +101,8 @@ agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat -cttgtacacgtcctgcagcggc ->p:HG002_1_chr20:63491489-63493165 +cttgtacacgtcctgcagcgg +>p:HG002_1_chr20:63491489-63493164 gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc actggctgggggtctcctatcagtgcccttctctggggtctcagatttgtttatggtttc tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg @@ -153,8 +153,8 @@ agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat -cttgtacacgtcctgcagcggc ->p:HG002_2_chr20:63491489-63493165 +cttgtacacgtcctgcagcgg +>p:HG002_2_chr20:63491489-63493164 gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc actggctgggggtctcctatcagtgcccttctctggggtctcagatttgtttatggtttc tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg @@ -205,8 +205,8 @@ agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat -cttgtacacgtcctgcagcggc ->ref_chr20:63491489-63493165 +cttgtacacgtcctgcagcgg +>ref_chr20:63491489-63493164 gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg @@ -257,4 +257,4 @@ agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat -cttgtacacgtcctgcagcggc +cttgtacacgtcctgcagcgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ff308abc6d0e72bcf1670b2c17001984.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_452bf94642317f3790592594df0a74e2.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_ff308abc6d0e72bcf1670b2c17001984.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_452bf94642317f3790592594df0a74e2.msa index 41aa4b4e..d9ae6133 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ff308abc6d0e72bcf1670b2c17001984.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_452bf94642317f3790592594df0a74e2.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63221380-63221977 +>syndip_1_chr20:63221380-63221976 tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc gcagtagcttc------------------------------------------------- @@ -16,8 +16,7 @@ gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc -t ->syndip_2_chr20:63221380-63221977 +>syndip_2_chr20:63221380-63221976 tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc gcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcagggag @@ -35,8 +34,7 @@ gattgcagggactgcagggcctgcattgctcttgcagcaccacccgcctccgtggacacc ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc -t ->p:HG002_1_chr20:63221380-63221977 +>p:HG002_1_chr20:63221380-63221976 tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc gcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcagggag @@ -54,8 +52,7 @@ gattgcagggactgcagggcctgcattgctcttgcagcaccacccgcctccgtggccacc ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc -t ->p:HG002_2_chr20:63221380-63221977 +>p:HG002_2_chr20:63221380-63221976 tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc gcagtagcttc------------------------------------------------- @@ -73,8 +70,7 @@ gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggccacc ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc -t ->ref_chr20:63221380-63221977 +>ref_chr20:63221380-63221976 tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc gcagtagcttc------------------------------------------------- @@ -92,4 +88,3 @@ gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc -t diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2783f53858aad63825027bab32e6c3bb.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_45f1dc1c7a33a6a5fbb511967c1352d7.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_2783f53858aad63825027bab32e6c3bb.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_45f1dc1c7a33a6a5fbb511967c1352d7.msa index b3aae3d8..867d45f9 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2783f53858aad63825027bab32e6c3bb.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_45f1dc1c7a33a6a5fbb511967c1352d7.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:8661844-8662220 +>syndip_1_chr20:8661844-8662219 atttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaa ccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatataattatataat tatttattatataattatatataattatataattatttattatataattatatataatta @@ -22,8 +22,8 @@ tttattacataagtatatatcacttattatataattgcatataattatttattatataat tgcatataa----ttattatataattgtatatagttatttattatataattg-------- -----------------tatatagttatttattatataattctatata-------attat ttattatctaattctatattaaatataattatttattatctaattctatattatatataa -ttatttattatataattctatattatatataattat ->syndip_2_chr20:8661844-8662220 +ttatttattatataattctatattatatataatta +>syndip_2_chr20:8661844-8662219 atttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaa ccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatataattatataat tatttattatataattatatataattatat------------------------------ @@ -47,8 +47,8 @@ tttattacataagtatatatcacttattatataattgtatataattatttattatataat tgcatataattatttattatataattgtatatagttatttattatataattctatatagt tatttattatataattctatataattatttattatctaattctatattatatataattat ttattatctaattctatattaaatataattatttattatctaattctatattatatataa -ttatttattatataattctatattatatataattat ->p:HG002_1_chr20:8661844-8662220 +ttatttattatataattctatattatatataatta +>p:HG002_1_chr20:8661844-8662219 atttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaa ccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatataattatataat tatttattatataattatatataattatat------------------------------ @@ -72,8 +72,8 @@ tttattacataagtatatatcacttattatataattgtatataattatttattatataat tgcatataattatttattatataattgtatatagttatttattatataattctatatagt tatatttattatacagttatataataaataattatataattatatataattatatattat ttattatctaattctatattaaatataattatttattatctaattctatattatatataa -ttatttattatataattctatattatatataattat ->p:HG002_2_chr20:8661844-8662220 +ttatttattatataattctatattatatataatta +>p:HG002_2_chr20:8661844-8662219 atttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaa ccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatataattatataat tatttattatataattatatataattatataattatttattatataattatatataa-ta @@ -97,8 +97,8 @@ tttattacataagtatatatcacttattatataattgcatataattatttattatataat tgcatataa----ttattatatatttat-----tatatttattatacagt---------- -----------------tatataataaataattatataattatatataattatatattat ttattatctaattctatattaaatataattatttattatctaattctatattatatataa -ttatttattatataattctatattatatataattat ->ref_chr20:8661844-8662220 +ttatttattatataattctatattatatataatta +>ref_chr20:8661844-8662219 atttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaa ccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatataattatataat tatttattatataattatatataattatat------------------------------ @@ -106,7 +106,7 @@ tatttattatataattatatataattatat------------------------------ taattatatatttattatatttat-----tatacagttatataataaataattatataat tatatataattatat-attatttattatctaattctat---------------------- -atta-aatataattatttattatctaattctatatta-tatataattatttattatata -attctatatta-tatataattat------------------------------------- +attctatatta-tatataatta-------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -122,4 +122,4 @@ attctatatta-tatataattat------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------- +----------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4857d0eafa15c85843680e3bfaf22f43.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4857d0eafa15c85843680e3bfaf22f43.msa deleted file mode 100644 index ca25e333..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4857d0eafa15c85843680e3bfaf22f43.msa +++ /dev/null @@ -1,165 +0,0 @@ ->syndip_1_chr20:60314230-60315121 -acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac -acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt -cctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc -catttgtccttccttccttccttccttccttccttccttccttccttccttccttccttc -cacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaaccatc -ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc -catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc -ctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatccact -cttccatccatccatccacccaccctt----------------ccatccatccatcctcc -catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc -ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc -catccatctaccctcccatccatccatcctcccacccaccctcccatccatccatcctcc -catcctcccatccatccatccatcctcccatccgtccatccatccttccatccac----- ------------cctcccatccatccatcctcccatccatctaccctcccatccatccatc -ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc -catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc -ataatctatcttcccatccatttgtccttccttccttccttccttccttccttccttcgt -tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca -tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca -t--------------------ccatcctcccatccatcctcccatcctcccatccattct -cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca -tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca -tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca -tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca -tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca -ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct -cccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt -cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca -tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca -tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag -ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat -gaaaaaaagaatatattgatttcaggccagttacataga ->syndip_2_chr20:60314230-60315121 -acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac -acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt -cgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc -catttg--------------------tccttccttccttccttccttccttccttccttc -cacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaaccatc -ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc -catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc -ctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatccacc -cttccatccatccatccacccacccttccatccatccatcctcccatccatccatcctcc -catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc -ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc -catccatctaccctcccatccatccatcctcccatccaccctcccatccatccatccatc -catccaccctctcatccatccatcctcccatccgtccatccatccttccatccaccctcc -catccatccatcctcccatccatccatcctcccatccatctaccctcccatccatccatc -ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc -catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc -ataatctatcttcccatccatttgtccttccttccttccttccttccttcc--------t -tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca -tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca -tccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatccattct -cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca -tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca -tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca -tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca -tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca -ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct -c----ccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt -cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca -tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca -tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag -ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat -gaaaaaaagaatatattgatttcaggccagttacataga ->p:HG002_1_chr20:60314230-60315121 -acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac -acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt -cgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc -catttg--------------------tccttccttccttccttccttccttccttccttc -cacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaaccatc -ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc -catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc -ctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatccacc -cttccatccatccatccacccacccttccatccatccatcctcccatccatccatcctcc -catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc -ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc -catccatctaccctcccatccatccatcctcccatccaccctcccatccatccatccatc -catccaccctctcatccatccatcctcccatccgtccatccatccttccatccaccctcc -catccatccatcctcccatccatccatcctcccatccatctaccctcccatccatccatc -ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc -catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc -ataatctatcttcccatccatttgtccttccttccttccttccttccttcc--------t -tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca -tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca -tccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatccattct -cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca -tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca -tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca -tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca -tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca -ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct -c----ccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt -cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca -tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca -tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag -ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat -gaaaaaaagaatatattgatttcaggccagttacataga ->p:HG002_2_chr20:60314230-60315121 -acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac -acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt -cctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc -catttgtccttccttccttccttccttccttccttccttccttccttccttccttccttc -cacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaaccatc -ctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatccatc -catccatcctcccatccatcctcccatccattatcccattcatccatcctcccatccatc -ctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatccact -cttccatccatccatccacccaccctt----------------ccatccatccatcctcc -catccatccatcctcccattcatctatccatccatccctcgatcctcccatccatccatc -ctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcctcc -catccatctaccctcccatccatccatcctcccacccaccctcccatccatccatcctcc -catcctcccatccatccatccatcctcccatccgtccatccatccttccatccac----- ------------cctcccatccatccatcctcccatccatctaccctcccatccatccatc -ctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatc -catccatcctcccatcctcccatccatccatcatccatccatccatccatccatcctccc -ataatctatcttcccatccatttgtccttccttccttccttccttccttccttccttcgt -tccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacca -tcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctatcca -t--------------------ccatcctcccatccatcctcccatcctcccatccattct -cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca -tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca -tccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctccca -tccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccatcca -tcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatcca -ccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcct -cccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt -cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca -tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca -tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag -ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat -gaaaaaaagaatatattgatttcaggccagttacataga ->ref_chr20:60314230-60315121 -acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac -acctgtacttccagctactcaggaggctgaggtggaaggattgaaa-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --atccatccatctgtcctcctacccatc---ctgctatccatccatccatccatcctccc -ataatctatcttcccatccatttgtccttccttccttccttccttccttcc--------t -tct---------------------tccttccttccttccttccttccttccacccatcca -tcctcccattcatcctcccatgcatcctc----ccatccatccacccaaccatcctccca -tccatcctcacatcgatcttcgcatccatccatcgatcgatctatccatccatccattct -cccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctccca -tccatccatcctcccatccatccacccttccatccatccatccacccacccttccatcca -tccaccctcccatccatccatcctcccat------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------ccatctatccatccatcctcccatcctcccatcct -cccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccatcgt -cccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccatcca -tcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccatcca -tccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgtgag -ttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaaaat -gaaaaaaagaatatattgatttcaggccagttacataga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_69e3cd763dbc4a7d135dbecb492d8b86.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_499b9b66e7735f3d7b3af193f2b77110.msa similarity index 99% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_69e3cd763dbc4a7d135dbecb492d8b86.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_499b9b66e7735f3d7b3af193f2b77110.msa index dbd71055..c3fc335d 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_69e3cd763dbc4a7d135dbecb492d8b86.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_499b9b66e7735f3d7b3af193f2b77110.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:64131813-64133957 +>syndip_1_chr20:64131813-64133956 tcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcat gtcctgtagagaccccctcactgtccactctcatggcctatagagaccccctcactgtca actctcatgtcctatg-agaccccctcactgtccactctcatggcctgtagagaccccct @@ -79,8 +79,8 @@ ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgta gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcat ggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc acccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatttgctc -cttgggttcccgg ->syndip_2_chr20:64131813-64133957 +cttgggttcccg +>syndip_2_chr20:64131813-64133956 tcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcat gtcctgtagagaccccctcactgtccactctcatggcctatagagaccccctcactgtcc accctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccct @@ -161,8 +161,8 @@ ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgt gtcctatagagaccccctcactgtccacccatatggcctgtagagaccccctcactgtcc acccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatttgctc -cttgggttcccgg ->p:HG002_1_chr20:64131813-64133957 +cttgggttcccg +>p:HG002_1_chr20:64131813-64133956 tcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcat gtcctgtagagaccccctcactgtccactctcatggcctatagagaccccctcactgtcc accctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccct @@ -243,8 +243,8 @@ ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgt ggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc acccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatttgctc -cttgggttcccgg ->p:HG002_2_chr20:64131813-64133957 +cttgggttcccg +>p:HG002_2_chr20:64131813-64133956 tcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcat gtcctgtagagaccccctcactgtccactctcatggcctatagagaccccctcactgtcc accctcatggcctgta-------------------------------------------- @@ -325,8 +325,8 @@ ctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctata gagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcat ggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc acccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatttgctc -cttgggttcccgg ->ref_chr20:64131813-64133957 +cttgggttcccg +>ref_chr20:64131813-64133956 tcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcat gtcctgtagagaccccctcactgtccactctcatggcctatagagaccccctcactgtcc accctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccct @@ -407,4 +407,4 @@ ctca-------------------------------------------------------- -----------------------------------------------------------t ggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc acccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatttgctc -cttgggttcccgg +cttgggttcccg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_686d29fdc617f6ce5cb3c1f76ee016c0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4cdf28703764613af970b6a20a9d76f8.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_686d29fdc617f6ce5cb3c1f76ee016c0.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_4cdf28703764613af970b6a20a9d76f8.msa index 61525439..7d784ca0 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_686d29fdc617f6ce5cb3c1f76ee016c0.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_4cdf28703764613af970b6a20a9d76f8.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:61201722-61202343 +>syndip_1_chr20:61201722-61202342 caggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctcca tcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgt caccgccatcctcactcaggaccctccatgagtgccacctccatcctcactcaggatccc @@ -24,8 +24,8 @@ accctccatgagtgtcacctccatc----ctcaggaccctccatg--------------- ctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat g-gtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcag gaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctccat ->syndip_2_chr20:61201722-61202343 +tcactcaggaccctcca +>syndip_2_chr20:61201722-61202342 caggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctcca tcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgt caccgccatcctcactcaggaccctccatgagtgccacctccatcctcac-caggatccc @@ -51,8 +51,8 @@ tcactcaggaccctccatggtgtcacctccatcctcactcaggacactccatggtgtcac ctccatccttactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccat gagtgccacctccatcctcac-caggatcccctgtaagtgtcacctccatcctcactcag gaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctccat ->p:HG002_1_chr20:61201722-61202343 +tcactcaggaccctcca +>p:HG002_1_chr20:61201722-61202342 caggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctcca tcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgt caccgccatcctcactcaggaccctccatgagtgccacctccatcctcac-caggatccc @@ -78,8 +78,8 @@ tcactcaggaccctccatggtgtcacctccatcctcactcaggacactccatagtgtcac ctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat g-gtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcag gaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctccat ->p:HG002_2_chr20:61201722-61202343 +tcactcaggaccctcca +>p:HG002_2_chr20:61201722-61202342 caggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctcca tcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgt caccgccatcctcactcaggaccctccatgagtgccacctccatcctcac-caggatccc @@ -105,8 +105,8 @@ accctccatgagtgtcacctccatc----ctcaggaccctccatg--------------- ctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat g-gtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcag gaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctccat ->ref_chr20:61201722-61202343 +tcactcaggaccctcca +>ref_chr20:61201722-61202342 caggaccctctgcggatgtcgcctccatcctcatcaggaccctccatg------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -132,4 +132,4 @@ accctccatgagtgtcacctccatc----ctcaggaccctccatg--------------- ctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat g-gtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcag gaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctccat +tcactcaggaccctcca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9f052ef8e75238e8dd45906b8a291987.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4eee85d5b4dd5f6e65e1aa2a72f439df.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_9f052ef8e75238e8dd45906b8a291987.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_4eee85d5b4dd5f6e65e1aa2a72f439df.msa index a00f7abb..25be5099 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9f052ef8e75238e8dd45906b8a291987.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_4eee85d5b4dd5f6e65e1aa2a72f439df.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63948414-63948859 +>syndip_1_chr20:63948414-63948858 acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga @@ -38,8 +38,8 @@ agagggagggggcgtgtgt--gagggaggggcgtgtgtgagaggga-ggggggcgtgtgt gagagggagggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt -gccactttgttgccataaaccaaaccgtagtctgt ->syndip_2_chr20:63948414-63948859 +gccactttgttgccataaaccaaaccgtagtctg +>syndip_2_chr20:63948414-63948858 acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga @@ -79,8 +79,8 @@ agagggaaggggcgtgtga--gagggaggggcgtgtgtgagaggga-ggggcgtgtgtga ga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt -gccactttgttgccataaaccaaaccgtagtctgt ->p:HG002_1_chr20:63948414-63948859 +gccactttgttgccataaaccaaaccgtagtctg +>p:HG002_1_chr20:63948414-63948858 acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga @@ -120,8 +120,8 @@ agagggaaggggcgtgtga--gagggaggggcgtgtgtgagaggga-ggggcgtgtgtga ga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt -gccactttgttgccataaaccaaaccgtagtctgt ->p:HG002_2_chr20:63948414-63948859 +gccactttgttgccataaaccaaaccgtagtctg +>p:HG002_2_chr20:63948414-63948858 acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga @@ -161,8 +161,8 @@ agagggagggggcgtgtgt--gagggaggggcgtgtgtgagaggga-ggggggcgtgtgt gagagggagggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt -gccactttgttgccataaaccaaaccgtagtctgt ->ref_chr20:63948414-63948859 +gccactttgttgccataaaccaaaccgtagtctg +>ref_chr20:63948414-63948858 acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc catgcgcctcg------------------------------------------------- @@ -202,4 +202,4 @@ agagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaaggggcgtgtgtga ga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt -gccactttgttgccataaaccaaaccgtagtctgt +gccactttgttgccataaaccaaaccgtagtctg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_69a6cc9af825b6514565ccdd59336cd0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_50a9c4a3245e4f0c0cab0597a64af000.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_69a6cc9af825b6514565ccdd59336cd0.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_50a9c4a3245e4f0c0cab0597a64af000.msa index 088b90c7..b4fced49 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_69a6cc9af825b6514565ccdd59336cd0.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_50a9c4a3245e4f0c0cab0597a64af000.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:62875072-62875657 +>syndip_1_chr20:62875072-62875656 aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac @@ -18,8 +18,8 @@ ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag -ctatcctgcc ->syndip_2_chr20:62875072-62875657 +ctatcctgc +>syndip_2_chr20:62875072-62875656 aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac @@ -39,8 +39,8 @@ ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag -ctatcctgcc ->p:HG002_1_chr20:62875072-62875657 +ctatcctgc +>p:HG002_1_chr20:62875072-62875656 aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac @@ -60,8 +60,8 @@ ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag -ctatcctgcc ->p:HG002_2_chr20:62875072-62875657 +ctatcctgc +>p:HG002_2_chr20:62875072-62875656 aactttcctggcacactggagaggacggcagaacgctggaatggatttatcgtgcaagac cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac @@ -81,8 +81,8 @@ ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag -ctatcctgcc ->ref_chr20:62875072-62875657 +ctatcctgc +>ref_chr20:62875072-62875656 aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt catcggggagc------------------------------------------------- @@ -102,4 +102,4 @@ ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag -ctatcctgcc +ctatcctgc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bd5862045dd8751a6c83a3c3d6321d88.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_513fe7d43fe32248d0e906427411d74f.msa similarity index 90% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_bd5862045dd8751a6c83a3c3d6321d88.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_513fe7d43fe32248d0e906427411d74f.msa index 4d33da27..6406e721 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_bd5862045dd8751a6c83a3c3d6321d88.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_513fe7d43fe32248d0e906427411d74f.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63371965-63372792 +>syndip_1_chr20:63371965-63372791 ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga @@ -12,8 +12,8 @@ attaaacgcccagggccactggcctgtccccagccccattaaacgcccagggccactgtc ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag -gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct ->syndip_2_chr20:63371965-63372792 +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcc +>syndip_2_chr20:63371965-63372791 ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga @@ -27,8 +27,8 @@ gccactgtcctgtccccagccccattaaacgcccagggccactgt--------------- ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag -gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct ->p:HG002_1_chr20:63371965-63372792 +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcc +>p:HG002_1_chr20:63371965-63372791 ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga @@ -42,8 +42,8 @@ gccactgtcctgtccccagccccattaaacgcccagggccactgt--------------- ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag -gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct ->p:HG002_2_chr20:63371965-63372792 +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcc +>p:HG002_2_chr20:63371965-63372791 ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga @@ -57,8 +57,8 @@ attaaacgcccagggccactggcctgtccccagccccattaaacgcccagggccactgtc ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag -gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct ->ref_chr20:63371965-63372792 +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcc +>ref_chr20:63371965-63372791 ggtcaggtgaagactctattcctggctcaggaaaaccaccaggacaggtgagcccagcag catctcgtggagggaggctctgagtcccgtgaggacaaggacggaacaccggggctgcca caggtcgcagagaccctgtgtcaacacccttgttttgaggtgcagagaccaaagttgaga @@ -72,4 +72,4 @@ attaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccactgtc ctgtccccagccccattaaacgcccagggccactggcctgtccccagccccattaaatgc ccagggccactgtcctgtccccagtctcattaaacgcagcaaacgtcttctggacgtgcc gccagtcccacagaaaaccaaagcaaggcagactcaccgctcctgcatcccggagctcag -gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcct +gtccaggagggtctcgggaaaggatgggggcaactggagtaccatcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_14df5b1a78900153927390d7bafee41c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5179b77bf332da7c07500c14adccd838.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_14df5b1a78900153927390d7bafee41c.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_5179b77bf332da7c07500c14adccd838.msa index d154fe9a..f9079649 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_14df5b1a78900153927390d7bafee41c.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_5179b77bf332da7c07500c14adccd838.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:38123490-38124806 +>syndip_1_chr20:38123490-38124805 ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa @@ -33,8 +33,8 @@ tatatatgtattatattattatagatataatatacatattatatctatatataaaatata tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg -tagagatggggtttcgccatgttgccgaggctggtgtcaa ->syndip_2_chr20:38123490-38124806 +tagagatggggtttcgccatgttgccgaggctggtgtca +>syndip_2_chr20:38123490-38124805 ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa @@ -69,8 +69,8 @@ tatatatgtattatattattatagatataatatacatattatatctatatataaaatata tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg -tagagatggggtttcgccatgttgccgaggctggtgtcaa ->p:HG002_1_chr20:38123490-38124806 +tagagatggggtttcgccatgttgccgaggctggtgtca +>p:HG002_1_chr20:38123490-38124805 ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa @@ -105,8 +105,8 @@ tatatatgtattatattattatagatataatatacatattatatctatatataaaatata tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg -tagagatggggtttcgccatgttgccgaggctggtgtcaa ->p:HG002_2_chr20:38123490-38124806 +tagagatggggtttcgccatgttgccgaggctggtgtca +>p:HG002_2_chr20:38123490-38124805 ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa @@ -141,8 +141,8 @@ tatatatgtattatattattatagatataatatacatattatatctatatataaaatata tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg -tagagatggggtttcgccatgttgccgaggctggtgtcaa ->ref_chr20:38123490-38124806 +tagagatggggtttcgccatgttgccgaggctggtgtca +>ref_chr20:38123490-38124805 ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg tcctgtaacctctctgggcctcagaaacctctctctctctctatatatatatatatataa @@ -177,4 +177,4 @@ tatatatgtattatattattatagatataatatacatattatatctatatataaaatata tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg -tagagatggggtttcgccatgttgccgaggctggtgtcaa +tagagatggggtttcgccatgttgccgaggctggtgtca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c95ab5f466d7144d537fb37124016439.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_541535ac45889f61485b69c44137fd45.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_c95ab5f466d7144d537fb37124016439.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_541535ac45889f61485b69c44137fd45.msa index 4f85bc90..a244f140 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c95ab5f466d7144d537fb37124016439.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_541535ac45889f61485b69c44137fd45.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:14861954-14862745 +>syndip_1_chr20:14861954-14862744 gacattggaggttttatatataaatatatatatatatatttatatatatatttatatata tatatttatatatatttatatatatttatatatatatttatatatatat--ttatatata tatttatatatatatttatatatatatttatatatatatttatatatatatttatatata @@ -25,8 +25,8 @@ aaatatatataaatatatatataaatataaatatatataaatata----taaaaatatat atataaatataaatatatataaatatatatgtataaatatatatataa----------at ataaatatatatatataaatatatatataaatatatatatataaatatatatataaatat atataaatatatatataaatatatataaatatatatatatatatttttttttaatagaga -ggatgaagaccaa ->syndip_2_chr20:14861954-14862745 +ggatgaagacca +>syndip_2_chr20:14861954-14862744 gacattggaggtttt--------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ @@ -53,8 +53,8 @@ aaatatataaaaatatatatataaatataaatatatataaatatatatgtataaatatat atataaatataaatatatataaatatatatatataaatatatatataa----------at atatataaatatatataaaaatatatataa--atatatatataaatatatatataaatat atataaatatatatataaatatatataaatatatatatatatatttttttttaatagaga -ggatgaagaccaa ->p:HG002_1_chr20:14861954-14862745 +ggatgaagacca +>p:HG002_1_chr20:14861954-14862744 gacattggaggtttt--------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ @@ -81,8 +81,8 @@ aaatatataaaaatatatatataaatataaatatatataaatatatatgtataaatatat atataaatataaatatatataaatatatatatataaatatatatataa----------at atatataaatatatataaaaatatatataa--atatatatataaatatatatataaatat atataaatatatatataaatatatataaatatatatatatatatttttttttaatagaga -ggatgaagaccaa ->p:HG002_2_chr20:14861954-14862745 +ggatgaagacca +>p:HG002_2_chr20:14861954-14862744 gacattggaggttttatatataaatatatatatatatatttatatatatatttatatata tatatttatatatatttatatatatttatatatatatttatatatatataaatatatata aatatataaatatatataaatatatatttatacataaatatataaatatatttatatata @@ -109,8 +109,8 @@ aaatatatataaatatatatataaatataaatatatataaatata----taaaaatatat atataaatataaatatatataaatatatatgtataaatatatatataa----------at ataaatatatatatataaatatatatataaatatatatatataaatatatatataaatat atataaatatatatataaatatatataaatatatatatatatatttttttttaatagaga -ggatgaagaccaa ->ref_chr20:14861954-14862745 +ggatgaagacca +>ref_chr20:14861954-14862744 gacattggaggttt---------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ @@ -137,4 +137,4 @@ aaatatatataaatatatatataaatataaatatatataaatata----taaaaatatat atataaatataaatatatataaatatatatgtataaatatatatataaatataaatatat ataaatatatatatataaatatatatataaatatatatatataaatatatatataaatat atataaatatatatataaatatatataaatatatatatatatatttttttttaatagaga -ggatgaagaccaa +ggatgaagacca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_efa1c6acccfa7bcd26ee40e0acbbc623.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_558c505e413a6398b429691dca26a4ea.msa similarity index 79% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_efa1c6acccfa7bcd26ee40e0acbbc623.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_558c505e413a6398b429691dca26a4ea.msa index 4480a3ba..0e524eae 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_efa1c6acccfa7bcd26ee40e0acbbc623.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_558c505e413a6398b429691dca26a4ea.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:62830550-62830798 +>syndip_1_chr20:62830550-62830797 ccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcagg aagctcccctgcaccccctctacccatgtaccacagtcccccaccccccaccgtgctcca ccccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtccccca @@ -6,9 +6,9 @@ accccaccacagtcccccaccccctaccacagtcccccaccccctaccacagtcccccaa cccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtccctcaac ccccaccacagtcccccaacccccatgacagtcccccaacccccaccacagtcccccaac ccccaccacagt-ccccaccccctaccacagtcccccaacccccaccacagtcccccacc -ccctaccacaatcccccaccccccac---------------------------------- ---------------------------------------------- ->syndip_2_chr20:62830550-62830798 +ccctaccacaatcccccacccccca----------------------------------- +-------------------------------------------- +>syndip_2_chr20:62830550-62830797 ccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcagg aagctcccctgcaccccctctacccatgtaccacagtccccca----------------- ccccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtccccca @@ -17,8 +17,8 @@ cccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtcccccaac ccccaccacagtccccc-acccccaccacagtccgccaacccccatgacagtcccccaac ccccaccacagtcccccaacccccatgacagtcccccaacccccaccacagtcccccaac ccctaccacagtcccccaacccccaccacagtccccaccccctaccacagtcccccaacc -cccaccacagtcccccaccccctaccacaatcccccaccccccac ->p:HG002_1_chr20:62830550-62830798 +cccaccacagtcccccaccccctaccacaatcccccacccccca +>p:HG002_1_chr20:62830550-62830797 ccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcagg aagctcccctgcaccccctctacccatgtaccacagtccccca----------------- ccccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtccccca @@ -27,8 +27,8 @@ cccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtcccccaac ccccaccacagtccccc-acccccaccacagtccgccaacccccatgacagtcccccaac ccccaccacagtcccccaacccccatgacagtcccccaacccccaccacagtcccccaac ccctaccacagtcccccaacccccaccacagtccccaccccctaccacagtcccccaacc -cccaccacagtcccccaccccctaccacaatcccccaccccccac ->p:HG002_2_chr20:62830550-62830798 +cccaccacagtcccccaccccctaccacaatcccccacccccca +>p:HG002_2_chr20:62830550-62830797 ccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcagg aagctcccctgcaccccctctacccatgtaccacagtcccccaccccccaccgtgctcca ccccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtccccca @@ -36,15 +36,15 @@ accccaccacagtcccccaccccctaccacagtcccccaccccctaccacagtcccccaa cccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtcccccaac ccccaccacagtcccccaacccccatgacagtcccccaacccctaccacagtcccccaac ccccaccacagt-ccccaccccctaccacagtcccccaacccccaccacagtcccccacc -ccctaccacaatcccccaccccccac---------------------------------- ---------------------------------------------- ->ref_chr20:62830550-62830798 +ccctaccacaatcccccacccccca----------------------------------- +-------------------------------------------- +>ref_chr20:62830550-62830797 ccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcagg aagctcccctgcaccccctctacccatgtaccacagtccccca----------------- -cccccatgacagtcccccaacccccaccacagtcccccaacccctaccacagtccccca acccccaccacagtccccaccccctaccacagtcccccaacccccaccacagtcccccac -cccctaccacaatcccccaccccccac--------------------------------- +cccctaccacaatcccccacccccca---------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ---------------------------------------------- +-------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b9d356b09aad1b84d7626c820eace838.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5b9c7d30d7119b8ee01d9d2df56da7df.msa similarity index 93% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_b9d356b09aad1b84d7626c820eace838.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_5b9c7d30d7119b8ee01d9d2df56da7df.msa index 320047f1..b1b3db87 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b9d356b09aad1b84d7626c820eace838.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_5b9c7d30d7119b8ee01d9d2df56da7df.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:35579913-35580987 +>syndip_1_chr20:35579913-35580986 aaaactccatctcaaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaaga ctgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgct gtcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggca @@ -21,8 +21,8 @@ ataaaatatatatatataaaatatatatataaaatatatatatataaaatatatatatat aaaatatatatatataaaatatatatatataaaatatatatataaaatatatatatataa aatatatatatataaaatatatatatataaaatatatatatggaattccatatctatcaa tggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtag -atatatacatatatacacatatatatgacaattttagcacaaaagagaggaa ->syndip_2_chr20:35579913-35580987 +atatatacatatatacacatatatatgacaattttagcacaaaagagagga +>syndip_2_chr20:35579913-35580986 aaaactccatctcaaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaaga ctgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgct gtcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggca @@ -45,8 +45,8 @@ atat---------------aaaatatatataaaatatatatatataaaatatatatatat aaaatatatatatataaaatat-------------------------------------- ----------------atatatatatataaaatatatatatggaattccatatctatcaa tggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtag -atatatacatatatacacatatatatgacaattttagcacaaaagagaggaa ->p:HG002_1_chr20:35579913-35580987 +atatatacatatatacacatatatatgacaattttagcacaaaagagagga +>p:HG002_1_chr20:35579913-35580986 aaaactccatctcaaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaaga ctgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgct gtcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggca @@ -69,8 +69,8 @@ atat---------------aaaatatatataaaatatatatatataaaatatatatatat aaaatatatatatataaaatat-------------------------------------- ----------------atatatatatataaaatatatatatggaattccatatctatcaa tggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtag -atatatacatatatacacatatatatgacaattttagcacaaaagagaggaa ->p:HG002_2_chr20:35579913-35580987 +atatatacatatatacacatatatatgacaattttagcacaaaagagagga +>p:HG002_2_chr20:35579913-35580986 aaaactccatctcaaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaaga ctgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgct gtcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggca @@ -93,8 +93,8 @@ ataaaatatatatatataaaatatatatataaaatatatatatataaaatatatatatat aaaatatatatatataaaatatatatatataaaatatatatataaaatatatatatataa aatatatatatataaaatatatatatataaaatatatatatggaattccatatctatcaa tggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtag -atatatacatatatacacatatatatgacaattttagcacaaaagagaggaa ->ref_chr20:35579913-35580987 +atatatacatatatacacatatatatgacaattttagcacaaaagagagga +>ref_chr20:35579913-35580986 aaaactccatctc-aaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaaga ctgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgct gtcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggca @@ -117,4 +117,4 @@ ataa---------------aatatatatatataatatatatatataaaatatatatatat aaaatatatatatatataaaat-------------------------------------- ----------------atatatatatataaaatatatatatggaattccatatctatcaa tggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtag -atatatacatatatacacatatatatgacaattttagcacaaaagagaggaa +atatatacatatatacacatatatatgacaattttagcacaaaagagagga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_918ac60720a8b1e5a939e5ef71c3dd30.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5f56f463de2082f8d7163ff2aada8742.msa similarity index 89% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_918ac60720a8b1e5a939e5ef71c3dd30.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_5f56f463de2082f8d7163ff2aada8742.msa index 7ce5f8b5..ad321691 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_918ac60720a8b1e5a939e5ef71c3dd30.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_5f56f463de2082f8d7163ff2aada8742.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:57110112-57110886 +>syndip_1_chr20:57110112-57110885 agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct @@ -11,8 +11,8 @@ tgggcgtgtgcggggc-------------------------------------------- cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct -gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca ->syndip_2_chr20:57110112-57110886 +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttc +>syndip_2_chr20:57110112-57110885 agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct @@ -25,8 +25,8 @@ tgggcgtgtgcggggc-------------------------------------------- cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct -gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca ->p:HG002_1_chr20:57110112-57110886 +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttc +>p:HG002_1_chr20:57110112-57110885 agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct @@ -39,8 +39,8 @@ tgggcgtgtgcggggc-------------------------------------------- cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct -gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca ->p:HG002_2_chr20:57110112-57110886 +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttc +>p:HG002_2_chr20:57110112-57110885 agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct @@ -53,8 +53,8 @@ tgggcgtgtgcggggc-------------------------------------------- cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct -gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca ->ref_chr20:57110112-57110886 +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttc +>ref_chr20:57110112-57110885 agaaaaatcctccagaagatgacagttccagttgatgggactgacaagccccccacagga aggcagtctccagctgaccactgttccgtgaggctgtctgagcaggcttcgctatgcacg cataatagcgacagcgcaaacagcagcagcagcagcagcctcagctggctcggcggggct @@ -67,4 +67,4 @@ gtgctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcgg cgtgtgcggggcgttatgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtct tccggttcggcgtgtgcggggcgctgtgctaagtcttccggctgcattcgcactctttcc ctccgactcaaccatggcagtgaggcactgttttgttttgctttgcttctcaattttcct -gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttca +gtggtaaaatacacctaatattcaccatcttaaccgtttttaagtgtacagttc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d00295e693e29721bd316e2a98d6b49d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6125f7292d70d0bf730d50e79d9e5f9d.msa similarity index 92% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_d00295e693e29721bd316e2a98d6b49d.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_6125f7292d70d0bf730d50e79d9e5f9d.msa index ac205f8c..a524e701 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d00295e693e29721bd316e2a98d6b49d.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_6125f7292d70d0bf730d50e79d9e5f9d.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63559188-63560064 +>syndip_1_chr20:63559188-63560063 tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt @@ -13,8 +13,8 @@ gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg -ccgctggtccaggtcgctcttggcacaggtgcggacg ->syndip_2_chr20:63559188-63560064 +ccgctggtccaggtcgctcttggcacaggtgcggac +>syndip_2_chr20:63559188-63560063 tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt @@ -29,8 +29,8 @@ gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg -ccgctggtccaggtcgctcttggcacaggtgcggacg ->p:HG002_1_chr20:63559188-63560064 +ccgctggtccaggtcgctcttggcacaggtgcggac +>p:HG002_1_chr20:63559188-63560063 tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt @@ -45,8 +45,8 @@ gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac gttcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg -ccgctggtccaggtcgctcttggcacaggtgcggacg ->p:HG002_2_chr20:63559188-63560064 +ccgctggtccaggtcgctcttggcacaggtgcggac +>p:HG002_2_chr20:63559188-63560063 tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt @@ -61,8 +61,8 @@ gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac gttcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg -ccgctggtccaggtcgctcttggcacaggtgcggacg ->ref_chr20:63559188-63560064 +ccgctggtccaggtcgctcttggcacaggtgcggac +>ref_chr20:63559188-63560063 tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt @@ -77,4 +77,4 @@ gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg -ccgctggtccaggtcgctcttggcacaggtgcggacg +ccgctggtccaggtcgctcttggcacaggtgcggac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_04f59078ccc583035a295f8ad3526dbf.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6272ac8c11659a343276a77a33bea482.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_04f59078ccc583035a295f8ad3526dbf.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_6272ac8c11659a343276a77a33bea482.msa index 60256db1..080f1729 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_04f59078ccc583035a295f8ad3526dbf.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_6272ac8c11659a343276a77a33bea482.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:21721074-21721836 +>syndip_1_chr20:21721074-21721835 agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat @@ -20,8 +20,8 @@ acatatataac--------------------------atgtattacatatatgtaataca tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc -ctcccacctcaacctcct ->syndip_2_chr20:21721074-21721836 +ctcccacctcaacctcc +>syndip_2_chr20:21721074-21721835 agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat @@ -43,8 +43,8 @@ acatatataacatatatgtaatacatatataacatatatgtattacatatatgtaataca tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc -ctcccacctcaacctcct ->p:HG002_1_chr20:21721074-21721836 +ctcccacctcaacctcc +>p:HG002_1_chr20:21721074-21721835 agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat @@ -66,8 +66,8 @@ acatatataacatatatgtaatacatatataacatatatgtattacatatatgtaataca tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc -ctcccacctcaacctcct ->p:HG002_2_chr20:21721074-21721836 +ctcccacctcaacctcc +>p:HG002_2_chr20:21721074-21721835 agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat @@ -89,8 +89,8 @@ acatatataac--------------------------atgtattacatatatgtaataca tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc -ctcccacctcaacctcct ->ref_chr20:21721074-21721836 +ctcccacctcaacctcc +>ref_chr20:21721074-21721835 agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat @@ -112,4 +112,4 @@ tatatatat--------------------------------------------------- ------------------------------------------------------------ --atataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc -ctcccacctcaacctcct +ctcccacctcaacctcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_be2ece84b9803ee6d8b5da47e0f1328a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_649eba2ef8750104fb27abd65692f3e5.msa similarity index 90% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_be2ece84b9803ee6d8b5da47e0f1328a.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_649eba2ef8750104fb27abd65692f3e5.msa index f88555c4..f47c531d 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_be2ece84b9803ee6d8b5da47e0f1328a.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_649eba2ef8750104fb27abd65692f3e5.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:62360310-62360703 +>syndip_1_chr20:62360310-62360702 gtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtg ggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtgggtgga tagggagggggtggggtgggtgcataggtaggggggtggatgggtcagcaggcagcggga @@ -9,8 +9,8 @@ gtgggtgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgggtgg tgggtgggtggagggatagatgggtggatgggtgggtagaaggataggta---ggtgggt gggtgggtggatggataggtgggtgggtgggtggaggaata--------gatgggtgggt ggatgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgggtgggt -gggtggagggaccacttcccaggtggagtgga ->syndip_2_chr20:62360310-62360703 +gggtggagggaccacttcccaggtggagtgg +>syndip_2_chr20:62360310-62360702 gtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtg ggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtggaggga tagatgggt--------------------------------------------------- @@ -21,8 +21,8 @@ gtgggtgggtgggtggaggaataga--------tgggtgggtgga--------------- tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg---ggtgggt gggtggaggga------------------------------------------------- ------------------------------------------------------------ ------------ccacttcccaggtggagtgga ->p:HG002_1_chr20:62360310-62360703 +-----------ccacttcccaggtggagtgg +>p:HG002_1_chr20:62360310-62360702 gtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtg ggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtggaggga tgggtg------------------------------------------------------ @@ -33,8 +33,8 @@ gtggg----------------------------tgggtgggtgga--------------- tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg---ggtgggt gggtggaggga------------------------------------------------- ------------------------------------------------------------ ------------ccacttcccaggtggagtgga ->p:HG002_2_chr20:62360310-62360703 +-----------ccacttcccaggtggagtgg +>p:HG002_2_chr20:62360310-62360702 gtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtg ggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtggaggga tgggtgagtgggtgggtggagggatagatgggtgggtggatgggtcagcaggcagcggga @@ -45,8 +45,8 @@ gtgggtgggtgggtggagggataga--------tgggtgggtggagggatagatgggtgg tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgggtggtgggt gggtggagggatagatgggtggatgggtgggtagaaggataggtaggtgggtgggtgggt ggatgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgggtgggt -gggtggagggaccacttcccaggtggagtgga ->ref_chr20:62360310-62360703 +gggtggagggaccacttcccaggtggagtgg +>ref_chr20:62360310-62360702 gtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtg ggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtggaggga tgggtg------------------------------------------------------ @@ -57,4 +57,4 @@ gtggg----------------------------tgggtgggtgga--------------- tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg---ggtgggt gggtggaggga------------------------------------------------- ------------------------------------------------------------ ------------ccacttcccaggtggagtgga +-----------ccacttcccaggtggagtgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_709f39dc3727958f3af64bf428a7aa8c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_66112df94acfa8f42760b311b37ff111.msa similarity index 88% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_709f39dc3727958f3af64bf428a7aa8c.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_66112df94acfa8f42760b311b37ff111.msa index 3b5e22b1..4d2cea0e 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_709f39dc3727958f3af64bf428a7aa8c.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_66112df94acfa8f42760b311b37ff111.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:57350708-57351088 +>syndip_1_chr20:57350708-57351087 aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta tttttagtactgacggggggacggggggacgggggacgggggacggggggcgggggggac @@ -7,8 +7,8 @@ ggggcggggggacgggggcggggggccggggggggcggggggacgggggcgggggggcgg ggggggcggggggacgggggcggggggcgcgggggggcggggggggcggcgcgggggggc gggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc -gcgcctggccagttgcggatttataaa ->syndip_2_chr20:57350708-57351088 +gcgcctggccagttgcggatttataa +>syndip_2_chr20:57350708-57351087 aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta tttttagtactgacggggggacgggggggc------------------------------ @@ -17,8 +17,8 @@ ggggcggggggacgggggcggggggcgggggggggc------------------------ -------------------------ggcgcgggggggc---------------------- -ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc -gcgcctggccagttgcggatttataaa ->p:HG002_1_chr20:57350708-57351088 +gcgcctggccagttgcggatttataa +>p:HG002_1_chr20:57350708-57351087 aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta tttttagtactgacggggggacgggggggc------------------------------ @@ -27,8 +27,8 @@ ggggcggggggacgggggcggggggcgggggggggc------------------------ -------------------------ggcgcgggggggc---------------------- -ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc -gcgcctggccagttgcggatttataaa ->p:HG002_2_chr20:57350708-57351088 +gcgcctggccagttgcggatttataa +>p:HG002_2_chr20:57350708-57351087 aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta tttttagtactgacggggggacggggggacgggggacgggggacggggggcgggggggac @@ -37,8 +37,8 @@ ggggcggggggacgggggcggggggccggggggggcggggggacgggggcgggggggcgg ggggggcggggggacgggggcggggggcgcgggggggcggggggggcggcgcgggggggc gggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc -gcgcctggccagttgcggatttataaa ->ref_chr20:57350708-57351088 +gcgcctggccagttgcggatttataa +>ref_chr20:57350708-57351087 aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta tttttagtactgacggggggacgggggggc------------------------------ @@ -47,4 +47,4 @@ ggggcggggggacgggggcggggggcgggggggggc------------------------ -------------------------ggcgcgggggggc---------------------- -ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc -gcgcctggccagttgcggatttataaa +gcgcctggccagttgcggatttataa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_16a9570a0bae9b86665a101c47ea2a7e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_69e7c4dc7f053eda2403927861e33459.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_16a9570a0bae9b86665a101c47ea2a7e.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_69e7c4dc7f053eda2403927861e33459.msa index 56d3b9e2..56caa352 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_16a9570a0bae9b86665a101c47ea2a7e.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_69e7c4dc7f053eda2403927861e33459.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63048933-63049513 +>syndip_1_chr20:63048933-63049512 gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat gtgggggcagactcctcctcctcctcctcttcctcctcc--------------------- @@ -20,8 +20,8 @@ tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca -ggacccagaagcctggtagaaagtgaccatgtgtggcaggt ->syndip_2_chr20:63048933-63049513 +ggacccagaagcctggtagaaagtgaccatgtgtggcagg +>syndip_2_chr20:63048933-63049512 gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat gtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctct @@ -43,8 +43,8 @@ tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca -ggacccagaagcctggtagaaagtgaccatgtgtggcaggt ->p:HG002_1_chr20:63048933-63049513 +ggacccagaagcctggtagaaagtgaccatgtgtggcagg +>p:HG002_1_chr20:63048933-63049512 gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat gtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctct @@ -66,8 +66,8 @@ tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca -ggacccagaagcctggtagaaagtgaccatgtgtggcaggt ->p:HG002_2_chr20:63048933-63049513 +ggacccagaagcctggtagaaagtgaccatgtgtggcagg +>p:HG002_2_chr20:63048933-63049512 gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat gtgggggcagactcctcctcctcctcctcttcctcctcc--------------------- @@ -89,8 +89,8 @@ tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca -ggacccagaagcctggtagaaagtgaccatgtgtggcaggt ->ref_chr20:63048933-63049513 +ggacccagaagcctggtagaaagtgaccatgtgtggcagg +>ref_chr20:63048933-63049512 gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat gtgggggcaga------------------------------------------------- @@ -112,4 +112,4 @@ tcctcctcctcctcttcctctcctcctcctcctcctcttcctcctcctcctcctcttcct cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca -ggacccagaagcctggtagaaagtgaccatgtgtggcaggt +ggacccagaagcctggtagaaagtgaccatgtgtggcagg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b4b5ccc01de0310c6839be1682c17fae.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6ab622358b0189242a15e470f601cb6b.msa similarity index 89% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_b4b5ccc01de0310c6839be1682c17fae.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_6ab622358b0189242a15e470f601cb6b.msa index 57e2e070..d87897ff 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b4b5ccc01de0310c6839be1682c17fae.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_6ab622358b0189242a15e470f601cb6b.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63221409-63221822 +>syndip_1_chr20:63221409-63221821 taagtaccagtgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctc agggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcag ggactgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattg @@ -12,8 +12,8 @@ cagggattgcagggactgcagggactgca------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ --------------------------------------------------------ttgc -tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctct ->syndip_2_chr20:63221409-63221822 +tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctc +>syndip_2_chr20:63221409-63221821 taagtaccagtgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctc agggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcag ggactgcagggattgcagggattgcagggagtgcagggactgcagggactgcagggattg @@ -27,8 +27,8 @@ cagggattgcagggattgcagggattgcagggactgcagggactgcagggattgcaggga ttgcagggattgcagggattgcagggattgcagggattgcagggactgcagggactgcag ggactgcagggattgcagggattgcagggattgcagggattgcagggactgcagggactg cagggattgcagggattgcagggattgcagggattgcagggactgcagggactgcattgc -tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctct ->p:HG002_1_chr20:63221409-63221822 +tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctc +>p:HG002_1_chr20:63221409-63221821 taagtaccagtgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctc agggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcag ggactgcagggattgcagggattgcagggattgcagggactgcagggattgcagggactg @@ -42,8 +42,8 @@ cagggattgcagggattgcagggattgcagggactgcagggactgcagggattgcaggga ttgcagggattgcagggattgcagggattgcagggattgcagggactgcagggactgcag ggactgcagggattgcagggattgcagggactgcagggactgcagggattgcagggactg cagggactgcagggactgcagggattgcagggattgcagggactgcagggactgcattgc -tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctct ->p:HG002_2_chr20:63221409-63221822 +tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctc +>p:HG002_2_chr20:63221409-63221821 taagtaccagtgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctc agggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcag ggactgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattg @@ -57,8 +57,8 @@ cagggattgcagggactgcagggactgca------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ --------------------------------------------------------ttgc -tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctct ->ref_chr20:63221409-63221822 +tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctc +>ref_chr20:63221409-63221821 taagtaccagtgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctc agggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcag ggactgcagggattgcagggattgcagggattgcagggactgcagggattgcagggactg @@ -72,4 +72,4 @@ ggactgcagggactgcagggattgcagggattgcagggactgcagggactgca------- ------------------------------------------------------------ ------------------------------------------------------------ --------------------------------------------------------ttgc -tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctct +tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6977cc03bff3fe04a12c3f85e1bf95f6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6c3ae6985541ddd1146ec32d22021912.msa similarity index 87% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_6977cc03bff3fe04a12c3f85e1bf95f6.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_6c3ae6985541ddd1146ec32d22021912.msa index 5c8f13d0..662f3074 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6977cc03bff3fe04a12c3f85e1bf95f6.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_6c3ae6985541ddd1146ec32d22021912.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:23155478-23155958 +>syndip_1_chr20:23155478-23155957 tcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaag aggaaggaaagcaagggaagggaaggggaggggaggaagggaaggggaggggaggaaggg aaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggag @@ -10,8 +10,8 @@ gaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaagagaaagaaagaaag aaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggaga gaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaagaagaa agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa -agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttg ->syndip_2_chr20:23155478-23155958 +agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacacctt +>syndip_2_chr20:23155478-23155957 tcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaag aggaaggaaagcaag-------------------ggaagggaaggggaggggaggaaggg aaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggag @@ -23,8 +23,8 @@ gaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag--------agaaag aaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggaga gaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag----- -------------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa -agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttg ->p:HG002_1_chr20:23155478-23155958 +agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacacctt +>p:HG002_1_chr20:23155478-23155957 tcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaag aggaaggaaagcaag-------------------ggaagggaaggggaggggaggaaggg aaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggag @@ -36,8 +36,8 @@ gaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag--------agaaag aaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggaga gaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag----- ---------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa -agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttg ->p:HG002_2_chr20:23155478-23155958 +agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacacctt +>p:HG002_2_chr20:23155478-23155957 tcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaag aggaaggaaagcaagggaagggaaggggaggggaggaagggaaggggaggggaggaaggg aaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggag @@ -49,8 +49,8 @@ gaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaagagaaagaaagaaag aaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggaga gaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaagaagaa agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa -agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttg ->ref_chr20:23155478-23155958 +agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacacctt +>ref_chr20:23155478-23155957 tcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaag aggaaggaaagcaag-------------------ggaagggaaggggaggggaggaaggg a----------------------------------------------------------- @@ -62,4 +62,4 @@ gaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag--------agaaag aaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggaga gaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag----- -------aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa -agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttg +agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacacctt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8df6edffbb5bd8f31a6e7d88b05e6592.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6fecb38e42c1fb0e27f26e0c7db37b3a.msa similarity index 92% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_8df6edffbb5bd8f31a6e7d88b05e6592.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_6fecb38e42c1fb0e27f26e0c7db37b3a.msa index 461d372c..12b6b8ba 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8df6edffbb5bd8f31a6e7d88b05e6592.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_6fecb38e42c1fb0e27f26e0c7db37b3a.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:10802576-10803059 +>syndip_1_chr20:10802576-10803058 gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca atgtcctctgaatatatatatatatatcctccc----------atatatatatatatcct @@ -7,8 +7,8 @@ ccc--atatatatatatatat--------------------------------------- tatatcctcccatatatatatctatcctccc----atatatatatatatatattttcaat gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca -caac ->syndip_2_chr20:10802576-10803059 +caa +>syndip_2_chr20:10802576-10803058 gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct @@ -17,8 +17,8 @@ cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca -caac ->p:HG002_1_chr20:10802576-10803059 +caa +>p:HG002_1_chr20:10802576-10803058 gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct @@ -27,8 +27,8 @@ cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca -caac ->p:HG002_2_chr20:10802576-10803059 +caa +>p:HG002_2_chr20:10802576-10803058 gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca atgtcctctgaatatatatatatatatcctccc----------atatatatatatatcct @@ -37,8 +37,8 @@ ccc--atatatatatatatat--------------------------------------- tatatcctcccatatatatatctatcctccc----atatatatatatatatattttcaat gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca -caac ->ref_chr20:10802576-10803059 +caa +>ref_chr20:10802576-10803058 gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct @@ -47,4 +47,4 @@ cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca -caac +caa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_05d37467dfbfe82df764ccf557e66822.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_71d3a3cbc7c7089cca081c650f00a2a6.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_05d37467dfbfe82df764ccf557e66822.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_71d3a3cbc7c7089cca081c650f00a2a6.msa index 36b5fec8..ac4698d9 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_05d37467dfbfe82df764ccf557e66822.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_71d3a3cbc7c7089cca081c650f00a2a6.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:50775444-50776124 +>syndip_1_chr20:50775444-50776123 tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc caaagatttcc--------------------atatatatatatatatatatataaatata @@ -12,8 +12,8 @@ taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa -tt ->syndip_2_chr20:50775444-50776124 +t +>syndip_2_chr20:50775444-50776123 tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata @@ -27,8 +27,8 @@ taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa -tt ->p:HG002_1_chr20:50775444-50776124 +t +>p:HG002_1_chr20:50775444-50776123 tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata @@ -42,8 +42,8 @@ taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa -tt ->p:HG002_2_chr20:50775444-50776124 +t +>p:HG002_2_chr20:50775444-50776123 tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc caaagatttcc--------------------atatatatatatatatatatataaatata @@ -57,8 +57,8 @@ taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa -tt ->ref_chr20:50775444-50776124 +t +>ref_chr20:50775444-50776123 tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata @@ -72,4 +72,4 @@ taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa -tt +t diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2cd0e934b9e98532ab4355e1842503c6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7253cbbea437a5ec4d1dc4d570629ba6.msa similarity index 83% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_2cd0e934b9e98532ab4355e1842503c6.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_7253cbbea437a5ec4d1dc4d570629ba6.msa index 220ba1f1..5d9682a7 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2cd0e934b9e98532ab4355e1842503c6.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_7253cbbea437a5ec4d1dc4d570629ba6.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:35580586-35580857 +>syndip_1_chr20:35580586-35580856 gcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaa tatatattatggtttattttattttatggttaaaggccatatatatatatatat-atata tatataatatatatatatataaaatatatatatataaaatatatatatatataaaatata @@ -8,30 +8,30 @@ ataaaatatatatatataaaatatatatatataaaatatatatatatataaaatatatat atataaaatatatatatataaaatatatatatatataatatatatatataaaatatatat atat--aaaatatatataaaatatatatatataaaatatatatataatatatatatataa aatatatatatataatatatatatataaaatatatatatataaaatatatatatatataa -aatatatatatatataaaatatatatatg ->syndip_2_chr20:35580586-35580857 +aatatatatatatataaaatatatatat +>syndip_2_chr20:35580586-35580856 gcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaa tatatattatggtttattttattttatggttaaaggccatatatatat---------ata tatatatataaaatatatataaaatatatatatata---------------------ata tatatataaaatatatatatat------aatatatatatataaaatatatatatataaaa -tatatatatatataaaatatatatatatataaaatatatatatg---------------- +tatatatatatataaaatatatatatatataaaatatatatat----------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------ ->p:HG002_1_chr20:35580586-35580857 +---------------------------- +>p:HG002_1_chr20:35580586-35580856 gcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaa tatatattatggtttattttattttatggttaaaggccatatatat-------------- ------------atatatataaaatatatatatataaaatatatatat------aatata tatatataaaatatatatatat------aatatatatatataaaatatatatatataaaa -tatatatatatataaaatatatatatatataaaatatatatatg---------------- +tatatatatatataaaatatatatatatataaaatatatatat----------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------ ->p:HG002_2_chr20:35580586-35580857 +---------------------------- +>p:HG002_2_chr20:35580586-35580856 gcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaa tatatattatggtttattttattttatggttaaaggccatatatatatatatataaaata tatatatataatatatatataaaatatatatatataaaatatatatatatataaaatata @@ -41,15 +41,15 @@ ataaaatatatatatataaaatatatatatataaaatatatatatatataaaatatatat atataaaatatatatatataaaatatatatatatataatatatatatataaaatatatat atataaaaaatatatataaaatatatatatataaaatatatatataatatatatatataa aatatatatatataatatatatatataaaatatatatatataaaatatatatatatataa -aatatatatatatataaaatatatatatg ->ref_chr20:35580586-35580857 +aatatatatatatataaaatatatatat +>ref_chr20:35580586-35580856 gcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaa tatatattatggtttattttattttatggttaaaggccatatatatatatatataaaata tatatatataaaatatatataaaatatatatatataaaatatatatat------aatata tatatataaaatatatatatat------aatatatatatataaaatatatatatataaaa -tatatatatatataaaatatatatatatataaaatatatatatg---------------- +tatatatatatataaaatatatatatatataaaatatatatat----------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------ +---------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_56e2cc0318de6e4a5452f63745c5e250.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7345416d874be507c2785df6e2e9361d.msa similarity index 92% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_56e2cc0318de6e4a5452f63745c5e250.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_7345416d874be507c2785df6e2e9361d.msa index 48276576..21091b0c 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_56e2cc0318de6e4a5452f63745c5e250.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_7345416d874be507c2785df6e2e9361d.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:35539020-35539825 +>syndip_1_chr20:35539020-35539824 tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat @@ -12,8 +12,8 @@ atataacagtttatatatataatatatataacagtttatatatataatatatataagttt atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga -aggggtgcagccagttctaggcagca ->syndip_2_chr20:35539020-35539825 +aggggtgcagccagttctaggcagc +>syndip_2_chr20:35539020-35539824 tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat @@ -27,8 +27,8 @@ atataacagtttatatatataatatatataacagtttatatatataatatatataagttt atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga -aggggtgcagccagttctaggcagca ->p:HG002_1_chr20:35539020-35539825 +aggggtgcagccagttctaggcagc +>p:HG002_1_chr20:35539020-35539824 tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat @@ -42,8 +42,8 @@ atataacagtttatatatataatatatataacagtttatatatataatatatataagttt atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga -aggggtgcagccagttctaggcagca ->p:HG002_2_chr20:35539020-35539825 +aggggtgcagccagttctaggcagc +>p:HG002_2_chr20:35539020-35539824 tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat @@ -57,8 +57,8 @@ atataacagtttatatatataatatatataacagtttatatatataatatatataagttt atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga -aggggtgcagccagttctaggcagca ->ref_chr20:35539020-35539825 +aggggtgcagccagttctaggcagc +>ref_chr20:35539020-35539824 tttttgtatttttagtagagacagggtttcaccatgttagccaggatggtcttgatctcc tgacctcgtgatccgcccgcctcggcctcccaaagtgctgggattacaggcgtgagccac agcgcccggcctatgttttacatatataacaatttatatataactacatatataatatat @@ -72,4 +72,4 @@ atataacagtttatatatataaaatatataacagtttatatatataatatatataagttt atatatataatatatataacagtttatatatattatatatatatatatgcacacacacaa agagagagagagagactcgctctgtcgcccaggctgtagtgcagtggtgtaatcacagct cactatgaggcaggagaacagggaatcagggtaaccgggggttaagacataagcaaatga -aggggtgcagccagttctaggcagca +aggggtgcagccagttctaggcagc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_756778e4a53861c2163701e9917f201a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_76652f704e7f5d8065ba92e110437e4d.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_756778e4a53861c2163701e9917f201a.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_76652f704e7f5d8065ba92e110437e4d.msa index 1f163e65..9b27e60f 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_756778e4a53861c2163701e9917f201a.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_76652f704e7f5d8065ba92e110437e4d.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:62057502-62058869 +>syndip_1_chr20:62057502-62058868 tacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcaca tcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaag gacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagc @@ -47,8 +47,8 @@ accaggccacagacaatggggctc-gggggccaacctcagcaagacctcaggaaggacgg acacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagac ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggcc aacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatg -gggctcgggggccaacctcagcaagacctcagga ->syndip_2_chr20:62057502-62058869 +gggctcgggggccaacctcagcaagacctcagg +>syndip_2_chr20:62057502-62058868 tacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcaca tcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaag gacggacacaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagc @@ -57,7 +57,7 @@ gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga caatggggctc-gggggccaacctcagcaagacctcaggaaggacggacacaggcctaca caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg acacaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagcaagac -ctcagga----------------------------------------------------- +ctcagg------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -97,8 +97,8 @@ ctcagga----------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------- ->p:HG002_1_chr20:62057502-62058869 +--------------------------------- +>p:HG002_1_chr20:62057502-62058868 tacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcaca tcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaag gacggacacaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagc @@ -107,7 +107,7 @@ gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg acacaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagcaagac -ctcagga----------------------------------------------------- +ctcagg------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -147,8 +147,8 @@ ctcagga----------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------- ->p:HG002_2_chr20:62057502-62058869 +--------------------------------- +>p:HG002_2_chr20:62057502-62058868 tacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcaca tcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaag gacggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagc @@ -197,8 +197,8 @@ accaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacgg acacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagac ctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctc-gggggcc aacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatg -gggctcgggggccaacctcagcaagacctcagga ->ref_chr20:62057502-62058869 +gggctcgggggccaacctcagcaagacctcagg +>ref_chr20:62057502-62058868 tacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcaca tcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaag gacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagc @@ -207,9 +207,9 @@ gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctaca caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg acacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagac -ctcagga----------------------------------------------------- +ctcagg------------------------------------------------------ ------------------------------------------------------------ -----------------------------------aggacggacacaggcctacacaccag +---------------------------------aaggacggacacaggcctacacaccag gccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacag gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga aggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctca @@ -224,7 +224,7 @@ gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacacca ggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacac aggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcag gaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcagga--------------------------------------------- +agcaagacctcagg---------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -247,4 +247,4 @@ agcaagacctcagga--------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------- +--------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0c9dec1fcbfa8df4c43412bac17355db.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7757219ce7f19ac23c5789d167c1c707.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_0c9dec1fcbfa8df4c43412bac17355db.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_7757219ce7f19ac23c5789d167c1c707.msa index b856638b..fb485d2f 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0c9dec1fcbfa8df4c43412bac17355db.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_7757219ce7f19ac23c5789d167c1c707.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:61282406-61283770 +>syndip_1_chr20:61282406-61283769 ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta @@ -26,8 +26,8 @@ tgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg tggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgt ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc -atttctttgtgatgggtcattagaagcaggattctgaatt ->syndip_2_chr20:61282406-61283770 +atttctttgtgatgggtcattagaagcaggattctgaat +>syndip_2_chr20:61282406-61283769 ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta @@ -55,8 +55,8 @@ ggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgctg tggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcat ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc -atttctttgtgatgggtcattagaagcaggattctgaatt ->p:HG002_1_chr20:61282406-61283770 +atttctttgtgatgggtcattagaagcaggattctgaat +>p:HG002_1_chr20:61282406-61283769 ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta @@ -84,8 +84,8 @@ ggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgctg tggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcat ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc -atttctttgtgatgggtcattagaagcaggattctgaatt ->p:HG002_2_chr20:61282406-61283770 +atttctttgtgatgggtcattagaagcaggattctgaat +>p:HG002_2_chr20:61282406-61283769 ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta @@ -113,8 +113,8 @@ tgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg tggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgt ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc -atttctttgtgatgggtcattagaagcaggattctgaatt ->ref_chr20:61282406-61283770 +atttctttgtgatgggtcattagaagcaggattctgaat +>ref_chr20:61282406-61283769 ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa tctttggcatggtgtgtgtgcatgtgtgtgtgtgtgtgtgtgtgtgtatgtctatctgta @@ -142,4 +142,4 @@ ggtgcatttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg tggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcat ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc -atttctttgtgatgggtcattagaagcaggattctgaatt +atttctttgtgatgggtcattagaagcaggattctgaat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bbd528e31e31fa673aa3dd6ff106fa0b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_783ef04c1562bdfce45b91b59fe4d678.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_bbd528e31e31fa673aa3dd6ff106fa0b.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_783ef04c1562bdfce45b91b59fe4d678.msa index 69a6d6b4..286d2d50 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_bbd528e31e31fa673aa3dd6ff106fa0b.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_783ef04c1562bdfce45b91b59fe4d678.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:641736-642566 +>syndip_1_chr20:641736-642565 atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc cccccaatctggttgcctgggaggggggcccagcgggggtggagttgcctgggggggggg @@ -22,8 +22,8 @@ ggggcccagcgggggtggagttgcctg-gggggggcccagcgggggtggagttgcctgtg ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct gggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg -tcgggcggggggcggcgctcgcagttccggaggggg ->syndip_2_chr20:641736-642566 +tcgggcggggggcggcgctcgcagttccggagggg +>syndip_2_chr20:641736-642565 atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg @@ -47,8 +47,8 @@ ggggcccagcgggggtggagttgcctgtgggggggcccagcgggggtggagttgcctgtg ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct -ggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg -tcgggcggggggcggcgctcgcagttccggaggggg ->p:HG002_1_chr20:641736-642566 +tcgggcggggggcggcgctcgcagttccggagggg +>p:HG002_1_chr20:641736-642565 atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg @@ -72,8 +72,8 @@ ggggcccagcgggggtggagttgcctgtgggggggcccagcgggggtggagttgcctgtg ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct -ggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg -tcgggcggggggcggcgctcgcagttccggaggggg ->p:HG002_2_chr20:641736-642566 +tcgggcggggggcggcgctcgcagttccggagggg +>p:HG002_2_chr20:641736-642565 atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc cccccaatctggttgcctgggaggggggcccagcgggggtggagttgcctgggggggggg @@ -97,8 +97,8 @@ ggggcccagcgggggtggagttgcctg-gggggggcccagcgggggtggagttgcctgtg ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct gggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg -tcgggcggggggcggcgctcgcagttccggaggggg ->ref_chr20:641736-642566 +tcgggcggggggcggcgctcgcagttccggagggg +>ref_chr20:641736-642565 atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg @@ -114,7 +114,7 @@ gggg----ccagcgggggtggagttgcctgggggggggccagcgggggtggagttgcctg tgggggggggccagcgggggtggagttgcctgggggggg----ccagcgggggtggagtt gcctgggggggg----ccagcgggggtggagcaccctggacggcccc--------gcgga gccccctgcgggaggcgagggcggccctcgggctctggaaggggccgcgcggcctggaag -acattacacggctgtcgggcggggggcggcgctcgcagttccggaggggg---------- +acattacacggctgtcgggcggggggcggcgctcgcagttccggagggg----------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -122,4 +122,4 @@ acattacacggctgtcgggcggggggcggcgctcgcagttccggaggggg---------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------- +----------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8b5baa0cc6e1948c19969dc20da6a9e8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_786136b3c2690bd2db0b1ed0059f1abd.msa similarity index 86% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_8b5baa0cc6e1948c19969dc20da6a9e8.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_786136b3c2690bd2db0b1ed0059f1abd.msa index 74fd3557..9be2c94a 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8b5baa0cc6e1948c19969dc20da6a9e8.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_786136b3c2690bd2db0b1ed0059f1abd.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:2240860-2241391 +>syndip_1_chr20:2240860-2241390 ctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcat cagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttc ctttctttctttctttttctttctttctctctctctccttccttccttctttccttccct @@ -9,8 +9,8 @@ cttccttcttccctccctccctctttgtttctttctttctctccctc------------- ------------------------------------------------------------ ----------------------cttccctccctccctttctttctcctt----------- ttcttccttccctccctgcctgtctccctctttctttctcttttttcttttccttccttc -cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttcttt ->syndip_2_chr20:2240860-2241391 +cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttctt +>syndip_2_chr20:2240860-2241390 ctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcat cagctcacttggaaaatgtagtcatcttctcaaagttttctt------------------ -tttctttctttctttttctttctttctctctctctccttccttccttctttccttccct @@ -21,8 +21,8 @@ cttccttcttccctccctccctctttgtttctttctttctctccctccttccctccctcc ctttcttccttctttccttatccctcccttctttccttccttccctttgtttctctttct ttctttctttctctctctcttccttccttccctccctccctccctccttcctcccttctt tccttccctccctgcctctctgtctccctctttctttctcttttttcttttccttccttc -cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttcttt ->p:HG002_1_chr20:2240860-2241391 +cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttctt +>p:HG002_1_chr20:2240860-2241390 ctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcat cagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttc ctttctttctttctttttctttctttctctctctctccttccttccttctttccttccct @@ -33,8 +33,8 @@ tttcttctttcttttcctccttcctcccttctttccttcccttcctt------------- ------------------------------------------------------------ ----------------------cttccctccctccctctttgtttctttctttctctccc tccttccctccctccctttctgtctccctctttctttctcttttttcttttccttccttc -cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttcttt ->p:HG002_2_chr20:2240860-2241391 +cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttctt +>p:HG002_2_chr20:2240860-2241390 ctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcat cagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttc ctttctttctttctttttctttctttctctctctctccttccttccttctttccttccct @@ -45,8 +45,8 @@ tttcttctttcttttcctccttcctcccttctttccttcccttcctt------------- ------------------------------------------------------------ ----------------------cttccctccctccctctttgtttctttctttctctccc tccttccctccctccctttctgtctccctctttctttctcttttttcttttccttccttc -cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttcttt ->ref_chr20:2240860-2241391 +cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttctt +>ref_chr20:2240860-2241390 ctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcat cagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttc ctttctttctttctttttctttctttctctctctctccttccttccttctttccttccct @@ -57,4 +57,4 @@ tttcttctttcttttcctccttcctcccttctttccttcccttcctt------------- ------------------------------------------------------------ ----------------------cttccctccctccctctttgtttctttctttctctccc tccttccctccctccctttctgtctccctctttctttctcttttttcttttccttccttc -cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttcttt +cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttctt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a4866977af1cc1005cd3c013448bd14b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7bb50c57d657828978076072c80f8a1f.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_a4866977af1cc1005cd3c013448bd14b.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_7bb50c57d657828978076072c80f8a1f.msa index 0f621360..79860f7c 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a4866977af1cc1005cd3c013448bd14b.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_7bb50c57d657828978076072c80f8a1f.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:18209039-18210235 +>syndip_1_chr20:18209039-18210234 tacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattc cagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacgatt ccttccacaccttccccacacccacacgaacctagacgattccttccacaccttccccac @@ -24,8 +24,8 @@ acacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaattc cttccacaccttccccacacccacacagacctagacgaattccttccacaccttct---- -------------------------------------ccacacccacacgaacctagaca attccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaaccta ->syndip_2_chr20:18209039-18210235 +cacacccacacaaacct +>syndip_2_chr20:18209039-18210234 tacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattc cagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacgatt ccttccacaccttccccacacccacacgaacctagacgattccttccacaccttccccac @@ -51,8 +51,8 @@ acacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaattc cttccacaccttccccacacccacacagacctagacgaattccttccacaccttct---- -------------------------------------ccacacccacacgaacctagaca attccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaaccta ->p:HG002_1_chr20:18209039-18210235 +cacacccacacaaacct +>p:HG002_1_chr20:18209039-18210234 tacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattc cagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacgatt ccttccacaccttccccacacccacacgaacctagacgattccttccacaccttccccac @@ -78,8 +78,8 @@ acacgaacctagacaattccttccacaccttcccacacccacacagacctagacgaattc cttccacaccttctccacacccacacgaacctagacg-attccttccacaccttcc---- -------------------------------------ccacacccacacgaacctagaca attccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaaccta ->p:HG002_2_chr20:18209039-18210235 +cacacccacacaaacct +>p:HG002_2_chr20:18209039-18210234 tacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattc cagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacgatt ccttccacaccttccccacacccacacgaacctagacgattccttccacaccttccccac @@ -105,8 +105,8 @@ acacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaattc cttccacaccttccccacacccacacagacctagacgaattccttccacaccttctccac acccacacgaacctagacgattccttccacaccttccccacacccacacgaacctagaca attccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaaccta ->ref_chr20:18209039-18210235 +cacacccacacaaacct +>ref_chr20:18209039-18210234 tacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattc cagtcccccaggcatgtatccttccgtagcttctccacacct------------------ -----------------------acacgaacctagacgattccttccacaccttccccac @@ -129,7 +129,7 @@ ccttccccacacccacacag---------------------------------------- -acctagacgaattccttccacaccttctccacacccacacgaacctagacg-attcctt ccacaccttccccacac-----------------------------------------cc acacgaacctagacaattccttgcacaccttctcacacccacacaaacctagacgaattc -cttccacaccttctccacacccacacaaaccta--------------------------- +cttccacaccttctccacacccacacaaacct---------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------- +----------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_861c06fcaf8a2444ad0e8a092dbbb547.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7ca10eb32dd50e600280f16b4afb82f5.msa similarity index 90% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_861c06fcaf8a2444ad0e8a092dbbb547.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_7ca10eb32dd50e600280f16b4afb82f5.msa index 0aa2b622..7f787dda 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_861c06fcaf8a2444ad0e8a092dbbb547.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_7ca10eb32dd50e600280f16b4afb82f5.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:57948698-57949591 +>syndip_1_chr20:57948698-57949590 cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg ccctgcacagatggacagatggttggaa----ggatggatggatggatggatggatggat @@ -13,8 +13,8 @@ gaatggatgatggatggatgaatgagatggatggatt------------gatggatggat ggatggatggaagaatggatgatggatggatgaatgagatgggtggattgatggatggat ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca -gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc ->syndip_2_chr20:57948698-57949591 +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctggg +>syndip_2_chr20:57948698-57949590 cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat @@ -29,8 +29,8 @@ gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca -gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc ->p:HG002_1_chr20:57948698-57949591 +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctggg +>p:HG002_1_chr20:57948698-57949590 cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat @@ -45,8 +45,8 @@ gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca -gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc ->p:HG002_2_chr20:57948698-57949591 +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctggg +>p:HG002_2_chr20:57948698-57949590 cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg ccctgcacagatggacagatggttggaa----ggatggatggatggatggatggatggat @@ -61,8 +61,8 @@ gaatggatgatggatggatgaatgagatggatggatt------------gatggatggat ggatggatggaagaatggatgatggatggatgaatgagatgggtggattgatggatggat ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca -gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc ->ref_chr20:57948698-57949591 +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctggg +>ref_chr20:57948698-57949590 cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat @@ -77,4 +77,4 @@ gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca -gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctgggc +gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_76590aeb93d34a21c775c3a21a1e3bdf.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7d4315446a621c1d4a1d8ccb36fdb130.msa similarity index 92% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_76590aeb93d34a21c775c3a21a1e3bdf.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_7d4315446a621c1d4a1d8ccb36fdb130.msa index 206e6406..f1266eda 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_76590aeb93d34a21c775c3a21a1e3bdf.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_7d4315446a621c1d4a1d8ccb36fdb130.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63154485-63155096 +>syndip_1_chr20:63154485-63155095 gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct @@ -9,8 +9,8 @@ caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca ---------------------tcccttcctcctcctccctccttcctccctcctccctcc tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg -tacaaggcagaaattg ->syndip_2_chr20:63154485-63155096 +tacaaggcagaaatt +>syndip_2_chr20:63154485-63155095 gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct @@ -21,8 +21,8 @@ caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg -tacaaggcagaaattg ->p:HG002_1_chr20:63154485-63155096 +tacaaggcagaaatt +>p:HG002_1_chr20:63154485-63155095 gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct @@ -33,8 +33,8 @@ caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg -tacaaggcagaaattg ->p:HG002_2_chr20:63154485-63155096 +tacaaggcagaaatt +>p:HG002_2_chr20:63154485-63155095 gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct @@ -45,8 +45,8 @@ caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca ---------------------tcccttcctcctcctccctccttcctccctcctccctcc tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg -tacaaggcagaaattg ->ref_chr20:63154485-63155096 +tacaaggcagaaatt +>ref_chr20:63154485-63155095 gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct @@ -57,4 +57,4 @@ caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg -tacaaggcagaaattg +tacaaggcagaaatt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_66a3a22d415ebc8e9c28636a422a27fb.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_83e1386bb11a239de07f648aed2478a4.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_66a3a22d415ebc8e9c28636a422a27fb.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_83e1386bb11a239de07f648aed2478a4.msa index f560985e..f81be9c5 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_66a3a22d415ebc8e9c28636a422a27fb.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_83e1386bb11a239de07f648aed2478a4.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:61744088-61744755 +>syndip_1_chr20:61744088-61744754 tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa aggagccaaccagagagtggggaggcgatggagagaataacagagaggaaggcaggtgca @@ -10,8 +10,8 @@ gggagagagatggaaagaggtggagggagagagagaaggaaagggagggaga-------- -------------------------gagagagacagacagacagcttcacacagacataa aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt -tcatcctg ->syndip_2_chr20:61744088-61744755 +tcatcct +>syndip_2_chr20:61744088-61744754 tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa aggagccaaccagagagtggggaggcgatggagagaataagagagaggaaggcaggtgca @@ -23,8 +23,8 @@ gagg-------------------------------------------------------- -------------------------gagagagagagacagacagcttcacacagacataa aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt -tcatcctg ->p:HG002_1_chr20:61744088-61744755 +tcatcct +>p:HG002_1_chr20:61744088-61744754 tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa aggagccaaccagagagtggggaggcgatggagagaataagagagaggaaggcaggtgca @@ -36,8 +36,8 @@ gagg-------------------------------------------------------- -------------------------gagagagagagacagacagcttcacacagacataa aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt -tcatcctg ->p:HG002_2_chr20:61744088-61744755 +tcatcct +>p:HG002_2_chr20:61744088-61744754 tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa aggagccaaccagagagtggggaggcgatggagagaataacagagaggaaggcaggtgca @@ -49,8 +49,8 @@ gggagagagatggaaagaggtggagggagagagagaaggaaagggagggaga-------- -------------------------gagagagacagacagacagcttcacacagacataa aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt -tcatcctg ->ref_chr20:61744088-61744755 +tcatcct +>ref_chr20:61744088-61744754 tcaaactgggcactgcaaattctggaatctctcctacctcccgaagtttgtagtccacca ggcccagggcgttctgaagcctggagggatgagaagcaagcggagactgtgtggttggaa aggagccaaccagagagtggggaggcgatggagagaataacagagaggaaggcaggtgca @@ -62,4 +62,4 @@ gaggggagaggaagagagggagagagagaaggagggagagagatggagagaggtggaggg agagagagaaggaaagggagggagagagagagacagacagacagcttcacacagacataa aacatctgctgttcaggatcccagctgccctccgactctgcctccttctaacccggctgc ctggctcacccgggtgacagggaggggcgccttcaccatgccctgtcctgaggctccctt -tcatcctg +tcatcct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_1c62e00ef65f42cbba04638af2263531.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_85836283fdfecd2a963f6b695137738c.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_1c62e00ef65f42cbba04638af2263531.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_85836283fdfecd2a963f6b695137738c.msa index 8de86f4e..a2467e55 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_1c62e00ef65f42cbba04638af2263531.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_85836283fdfecd2a963f6b695137738c.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:62349541-62349927 +>syndip_1_chr20:62349541-62349926 aagagggaggacaaaacagccgttttcagacaattccggatagactgtcatggaatagaa aaactacagggtgcatttcaggaaggaggaagcagcaacccaggggatggggatggggat ggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgat @@ -23,8 +23,8 @@ ggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcag------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------------------------------aaaattgctggctga ->syndip_2_chr20:62349541-62349927 +-------------------------------aaaattgctggctg +>syndip_2_chr20:62349541-62349926 aagagggaggacaaaacagccgttttcagacaattccggatagactgtcatggaatagaa aaactacagggtgcatttcaggaaggaggaagcagcaaccca------ggggatggggat ggggatggggatggggatggtgggggtgatgggggtgatgatggtgatggtgggggtgat @@ -49,8 +49,8 @@ ggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatg gtagaggtgatgatggtgggggtgatggtgggggtgggggtgggggtgggggtgatgatg gtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggggtgggg gtgggggtgggggtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtgg -gagtaaggtgatggtggaggtaaagaggcagaaaattgctggctga ->p:HG002_1_chr20:62349541-62349927 +gagtaaggtgatggtggaggtaaagaggcagaaaattgctggctg +>p:HG002_1_chr20:62349541-62349926 aagagggaggacaaaacagccgttttcagacaattccggatagactgtcatggaatagaa aaactacagggtgcatttcaggaaggaggaagcagcaaccca------ggggatggggat ggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgat @@ -75,8 +75,8 @@ ggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatg gtagaggtgatgatggtgggggtgatggtgggggtgggggtgggggtgggggtgatgatg gtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggggtggcg gtgatggtgggggtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtgg -gagtaaggtgatggtggaggtaaagaggcagaaaattgctggctga ->p:HG002_2_chr20:62349541-62349927 +gagtaaggtgatggtggaggtaaagaggcagaaaattgctggctg +>p:HG002_2_chr20:62349541-62349926 aagagggaggacaaaacagccgttttcagacaattccggatagactgtcatggaatagaa aaactacagggtgcatttcaggaaggaggaagcagcaaccca------ggggatggggat ggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgat @@ -101,8 +101,8 @@ ggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcag------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------------------------------aaaattgctggctga ->ref_chr20:62349541-62349927 +-------------------------------aaaattgctggctg +>ref_chr20:62349541-62349926 aagagggaggacaaaacagccgttttcagacaattccggatagactgtcatggaatagaa aaactacagggtgcatttcaggaaggaggaagcagcaaccca------ggggatggggat ggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgat @@ -127,4 +127,4 @@ ggagtaaggtgatggtggaggtaaagaggcag---------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------------------------------aaaattgctggctga +-------------------------------aaaattgctggctg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a6937b7b4931c9433881ec8a54af98fd.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_86dba3a0aeae01ccc8257baa7389c2b2.msa similarity index 73% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_a6937b7b4931c9433881ec8a54af98fd.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_86dba3a0aeae01ccc8257baa7389c2b2.msa index a8f660dc..d136d90a 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a6937b7b4931c9433881ec8a54af98fd.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_86dba3a0aeae01ccc8257baa7389c2b2.msa @@ -1,30 +1,30 @@ ->syndip_1_chr20:7720811-7721104 +>syndip_1_chr20:7720811-7721103 tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca aatgacattttctttttcttttcttttctttctttttttttttttttttgggatggagtt ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc -aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct ->syndip_2_chr20:7720811-7721104 +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagc +>syndip_2_chr20:7720811-7721103 tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca aatgacgttttctttttcttttc---------------tttttttttttgggatggagtt ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc -aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct ->p:HG002_1_chr20:7720811-7721104 +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagc +>p:HG002_1_chr20:7720811-7721103 tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca aatgacgttttctttttcttttc---------------tttttttttttgggatggagtt ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc -aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct ->p:HG002_2_chr20:7720811-7721104 +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagc +>p:HG002_2_chr20:7720811-7721103 tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca aatgacattttctttttcttttcttttctttctttttttttttttttttgggatggagtt ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc -aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct ->ref_chr20:7720811-7721104 +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagc +>ref_chr20:7720811-7721103 tcacacatttaagatacaattcctttccccaccccaactctccaggtttcctgaattaat tggaaggaaactgttatatttccttaattcctgaagtgggagttaaatctaaatctaaca aatgacattttctttttcttttcttttctttctttttttttttttttttgggatggagtt ccactcttgttgcccaggctggacaggctggaatacaatggcgtgatcttggctctctgc -aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagct +aacctccgactcccaggttcaagtgattctcctgcctcagcctcccaactagc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e42e2915a756c6b9535d501ffcc3f9b1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8a7bc612e0bdea73ad6aea0abc428b43.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_e42e2915a756c6b9535d501ffcc3f9b1.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_8a7bc612e0bdea73ad6aea0abc428b43.msa index 782feb92..1e6f680f 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e42e2915a756c6b9535d501ffcc3f9b1.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_8a7bc612e0bdea73ad6aea0abc428b43.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:44763796-44764386 +>syndip_1_chr20:44763796-44764385 gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc @@ -11,8 +11,8 @@ atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc atccacttatccatccacccatccatccatccgtccatccattcatccatccatccatcc tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa -tggggtcagtg ->syndip_2_chr20:44763796-44764386 +tggggtcagt +>syndip_2_chr20:44763796-44764385 gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc @@ -25,8 +25,8 @@ atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc atccatttatccatccacccatccatccatccgtccatccattcatccatccatccatcc tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa -tggggtcagtg ->p:HG002_1_chr20:44763796-44764386 +tggggtcagt +>p:HG002_1_chr20:44763796-44764385 gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc @@ -39,8 +39,8 @@ atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc atccatttatccatccacccatccatccatccgtccatccattcatccatccatccatcc tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa -tggggtcagtg ->p:HG002_2_chr20:44763796-44764386 +tggggtcagt +>p:HG002_2_chr20:44763796-44764385 gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc @@ -53,8 +53,8 @@ atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc atccacttatccatccacccatccatccatccgtccatccattcatccatccatccatcc tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa -tggggtcagtg ->ref_chr20:44763796-44764386 +tggggtcagt +>ref_chr20:44763796-44764385 gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc @@ -67,4 +67,4 @@ atccatccatccatccatccatccatccatccatttatcc-------------------- atccatccatccatccacccatccatccatccgtccatccattcatccatccatccatcc tcccacaaactcaccaagcctacaatgcaatcaattctgctgtaacatgaaatatacatt tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa -tggggtcagtg +tggggtcagt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3f97b2feb3fc3f1fe6d75a09563e2084.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8e86d26235c230b6c03a21914919f32d.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_3f97b2feb3fc3f1fe6d75a09563e2084.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_8e86d26235c230b6c03a21914919f32d.msa index c4967b74..ca0778f7 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3f97b2feb3fc3f1fe6d75a09563e2084.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_8e86d26235c230b6c03a21914919f32d.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:18208997-18210828 +>syndip_1_chr20:18208997-18210827 gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca @@ -34,8 +34,8 @@ tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg -ctggagtgcag ->syndip_2_chr20:18208997-18210828 +ctggagtgca +>syndip_2_chr20:18208997-18210827 gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca @@ -71,8 +71,8 @@ tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg -ctggagtgcag ->p:HG002_1_chr20:18208997-18210828 +ctggagtgca +>p:HG002_1_chr20:18208997-18210827 gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca @@ -108,8 +108,8 @@ tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg -ctggagttcag ->p:HG002_2_chr20:18208997-18210828 +ctggagttca +>p:HG002_2_chr20:18208997-18210827 gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca @@ -145,8 +145,8 @@ tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg -ctggagtgcag ->ref_chr20:18208997-18210828 +ctggagtgca +>ref_chr20:18208997-18210827 gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta tccttccgtagcttctccacacct------------------------------------ @@ -182,4 +182,4 @@ tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg -ctggagtgcag +ctggagtgca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8f0a476d665d82b7248a60d8b6288338.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8f0a476d665d82b7248a60d8b6288338.msa deleted file mode 100644 index 611f55b3..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8f0a476d665d82b7248a60d8b6288338.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:63641747-63642116 -acgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcctcggagtcc -ccggccccgctctgcgcccctccgagctccgccctagccccgcccccgcccagtgccccg -ccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccc -tggccccgccccggcccctgcccgctccgagctccgccctggccccgccccccgcccagt -gccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagct -ccgccccgg--------------------------------------------------- ------------------------------------------------------------- -----------------------ccccgccccggcccctgcccgctccgagctccgccctg -gccccgcccccgcccagtgccccgccccctgactgctgctagccctgcccccgccccggc -ccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctccgagctccg -ccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgccccggcccc -tgcccgctccgagctccgccccggccccgcccccgcaccttctcgcg ->syndip_2_chr20:63641747-63642116 -acgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcctcggagtcc -ccggccccgctctgcgcccctccgagctccgccctagccccgcccccgcccagtgccccg -ccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccc -cggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccccgcccagt -gccccgccccctgactgctgctagccctgcccccgccccggcccctgcccgctccgagct -ccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccc -tccccggcccctgcccgctccgagctccgccccggccccgccccggcccagtgccccgcc -ccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccctg -gccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccctccccggc -ccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctccgagcttcg -ccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgccccggcccc -tgcccgctccgagctccgccccggccccgcccccgcaccttctcgcg ->p:HG002_1_chr20:63641747-63642116 -acgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcctcggagtcc -ccggccccgctctgcgcccctccgagctccgccctagccccgcccccgcccagtgccccg -ccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccc -cggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccccgcccagt -gccccgccccctgactgctgctagccctgcccccgccccggcccctgcccgctccgagct -ccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccc -tccccggcccctgcccgctccgagctccgccccggccccgccccggcccagtgccccgcc -ccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccctg -gccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccctccccggc -ccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctccgagcttcg -ccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgccccggcccc -tgcccgctccgagctccgccccggccccgcccccgcaccttctcgcg ->p:HG002_2_chr20:63641747-63642116 -acgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcctcggagtcc -ccggccccgctctgcgcccctccgagctccgccctagccccgcccccgcccagtgccccg -ccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccc -cggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccccgcccagt -gccccgccccctgactgctgctagccctgcccccgccccggcccctgcccgctccgagct -ccgccccgg--------------------------------------------------- ------------------------------------------------------------- -----------------------ccccgccccggcccctgcccgctccgagctccgccctg -gccccgcccccgcccagtgccccgccccctgactgctgctagccctgcccccgccccggc -ccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctccgagctccg -ccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgccccggcccc -tgcccgctccgagctccgccccggccccgcccccgcaccttctcgcg ->ref_chr20:63641747-63642116 -acgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcctcggagtcc -ccggccccgctctgcgcccctccgagctccgccctagccccgcccccgcccagtgccccg -ccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccc -cggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccccgcccagt -gccccgccccctgactgctgctagccctgcccccgccccggcccctgcccgctccgagct -tcgccccgg--------------------------------------------------- ------------------------------------------------------------- -----------------------ccccgccccggcccctgcccgctccgagctccgccccg -gccccgcccccgcaccttctcgcg------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_eee9610d6083d41536c3c93d53b55f73.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8f863700689b63e4e012e6bd667b5518.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_eee9610d6083d41536c3c93d53b55f73.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_8f863700689b63e4e012e6bd667b5518.msa index 60de427f..4942c214 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_eee9610d6083d41536c3c93d53b55f73.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_8f863700689b63e4e012e6bd667b5518.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63535574-63536346 +>syndip_1_chr20:63535574-63536345 acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaaccac @@ -15,8 +15,8 @@ ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctgg cctcccgct-ccccccccacctggcctcccaccccctcctcacctggcctcctccccact tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc -tgctaacgaggtcgtgggtct ->syndip_2_chr20:63535574-63536346 +tgctaacgaggtcgtgggtc +>syndip_2_chr20:63535574-63536345 acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- @@ -33,8 +33,8 @@ ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc -tgctaacgaggtcgtgggtct ->p:HG002_1_chr20:63535574-63536346 +tgctaacgaggtcgtgggtc +>p:HG002_1_chr20:63535574-63536345 acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- @@ -51,8 +51,8 @@ ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc -tgctaacgaggtcgtgggtct ->p:HG002_2_chr20:63535574-63536346 +tgctaacgaggtcgtgggtc +>p:HG002_2_chr20:63535574-63536345 acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaaccac @@ -69,8 +69,8 @@ ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctgg cctcccgct-ccccccccacctggcctcccaccccctcctcacctggcctcctccccact tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc -tgctaacgaggtcgtgggtct ->ref_chr20:63535574-63536346 +tgctaacgaggtcgtgggtc +>ref_chr20:63535574-63536345 acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- @@ -87,4 +87,4 @@ ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc -tgctaacgaggtcgtgggtct +tgctaacgaggtcgtgggtc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8e66fbe0004e8e66a6d2f5eda4fc033d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9b9b387681fd363ece224e3813679abe.msa similarity index 91% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_8e66fbe0004e8e66a6d2f5eda4fc033d.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_9b9b387681fd363ece224e3813679abe.msa index cd1e16cd..80617d12 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8e66fbe0004e8e66a6d2f5eda4fc033d.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_9b9b387681fd363ece224e3813679abe.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:61561820-61562604 +>syndip_1_chr20:61561820-61562603 acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg @@ -14,8 +14,8 @@ tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg gaccccagggctcccggagagagagagggaccttcgtgtggagaggtggaccccaggact cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac -ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc ->syndip_2_chr20:61561820-61562604 +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagcc +>syndip_2_chr20:61561820-61562603 acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg @@ -31,8 +31,8 @@ tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac -ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc ->p:HG002_1_chr20:61561820-61562604 +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagcc +>p:HG002_1_chr20:61561820-61562603 acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg @@ -48,8 +48,8 @@ tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac -ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc ->p:HG002_2_chr20:61561820-61562604 +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagcc +>p:HG002_2_chr20:61561820-61562603 acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg @@ -65,8 +65,8 @@ tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg gaccccagggctcccggagagagagagggaccttcgtgtggagaggtggaccccaggact cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac -ttggtgcatccctgcaggatctgagcacagaacggcctgcttcagccc ->ref_chr20:61561820-61562604 +ttggtgcatccctgcaggatctgagcacagaacggcctgcttcagcc +>ref_chr20:61561820-61562603 acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg @@ -82,4 +82,4 @@ tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac -ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagccc +ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_06b42ffdbc8be646eb8718b5d6951dcc.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9e47b8fad37392ee138dfca4c2353754.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_06b42ffdbc8be646eb8718b5d6951dcc.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_9e47b8fad37392ee138dfca4c2353754.msa index 50ae4b6d..1b7c4215 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_06b42ffdbc8be646eb8718b5d6951dcc.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_9e47b8fad37392ee138dfca4c2353754.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:61100692-61102788 +>syndip_1_chr20:61100692-61102787 ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc @@ -36,8 +36,8 @@ acctggggagaccccgagtgagggcagatggccacatcctctaattcctgtgtcacacct ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta -aaaatgttatcaatttaataacattgatggttacagagctgtgtaa ->syndip_2_chr20:61100692-61102788 +aaaatgttatcaatttaataacattgatggttacagagctgtgta +>syndip_2_chr20:61100692-61102787 ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc @@ -75,8 +75,8 @@ acctggggagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta -aaaatgttatcaatttaataacattgatggttacagagctgtgtaa ->p:HG002_1_chr20:61100692-61102788 +aaaatgttatcaatttaataacattgatggttacagagctgtgta +>p:HG002_1_chr20:61100692-61102787 ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc @@ -114,8 +114,8 @@ acctggggagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta -aaaatgttatcaatttaataacattgatggttacagagctgtgtaa ->p:HG002_2_chr20:61100692-61102788 +aaaatgttatcaatttaataacattgatggttacagagctgtgta +>p:HG002_2_chr20:61100692-61102787 ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc @@ -153,8 +153,8 @@ acctggggagaccccgagtgagggcagatggccacatcctctaattcctgtgtcacacct ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta -aaaatgttatcaatttaataacattgatggttacagagctgtgtaa ->ref_chr20:61100692-61102788 +aaaatgttatcaatttaataacattgatggttacagagctgtgta +>ref_chr20:61100692-61102787 ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc @@ -192,4 +192,4 @@ acctggggagaccccgagtgagggcagatggccacatcctctaattcctgtgtcacacct ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta -aaaatgttatcaatttaataacattgatggttacagagctgtgtaa +aaaatgttatcaatttaataacattgatggttacagagctgtgta diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4d5d51153a3589a4d6cd04e486f7c879.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9e8a807906028744f45dff50046a00aa.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_4d5d51153a3589a4d6cd04e486f7c879.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_9e8a807906028744f45dff50046a00aa.msa index 55b397dc..ea31e8a0 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4d5d51153a3589a4d6cd04e486f7c879.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_9e8a807906028744f45dff50046a00aa.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:20337100-20337808 +>syndip_1_chr20:20337100-20337807 tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat @@ -35,8 +35,8 @@ ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt -tacaatcctgcctgcctctcacccagacctcttg ->syndip_2_chr20:20337100-20337808 +tacaatcctgcctgcctctcacccagacctctt +>syndip_2_chr20:20337100-20337807 tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat @@ -73,8 +73,8 @@ ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt -tacaatcctgcctgcctctcacccagacctcttg ->p:HG002_1_chr20:20337100-20337808 +tacaatcctgcctgcctctcacccagacctctt +>p:HG002_1_chr20:20337100-20337807 tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat @@ -111,8 +111,8 @@ ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt cttagcagacgtcccaccatggaagaggtcatggggcacaggggctttgggaaaggtgtt -tacaatcctgcctccctctcacccagacctcttg ->p:HG002_2_chr20:20337100-20337808 +tacaatcctgcctccctctcacccagacctctt +>p:HG002_2_chr20:20337100-20337807 tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat @@ -149,8 +149,8 @@ ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt cttagcagacgtcccaccatggaagaggtcatggggcacaggggctttgggaaaggtgtt -tacaatcctgcctccctctcacccagacctcttg ->ref_chr20:20337100-20337808 +tacaatcctgcctccctctcacccagacctctt +>ref_chr20:20337100-20337807 tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat @@ -187,4 +187,4 @@ ggatagaataaaaaagaaa----------------------------------------- ------------------------------------------------------------ --------------------------------------gctaggacatggttctagtgtt cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt -tacaatcctgcctgcctctcacccagacctcttg +tacaatcctgcctgcctctcacccagacctctt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4bb181db4c68004bc40764f9b6d76b42.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a2808b205fb6e4ff2a694b9b59fe99d7.msa similarity index 89% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_4bb181db4c68004bc40764f9b6d76b42.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_a2808b205fb6e4ff2a694b9b59fe99d7.msa index 5c387ca0..c5bff334 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4bb181db4c68004bc40764f9b6d76b42.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_a2808b205fb6e4ff2a694b9b59fe99d7.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:61289562-61290374 +>syndip_1_chr20:61289562-61290373 tgaccacaggccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttg gtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgct gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttg @@ -11,9 +11,9 @@ atgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatc caatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgta tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc -gatatccaatgagacttgctggatttatccc----------------------------- ---------------------------------- ->syndip_2_chr20:61289562-61290374 +gatatccaatgagacttgctggatttatcc------------------------------ +-------------------------------- +>syndip_2_chr20:61289562-61290373 tgaccacaggccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttg gtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgct gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttg @@ -27,8 +27,8 @@ caatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgta tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc cgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttatc -cc------------------------------- ->p:HG002_1_chr20:61289562-61290374 +c------------------------------- +>p:HG002_1_chr20:61289562-61290373 tgaccacaggccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttg gtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgct gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttg @@ -42,8 +42,8 @@ caatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgta tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc cgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttatc -cc------------------------------- ->p:HG002_2_chr20:61289562-61290374 +c------------------------------- +>p:HG002_2_chr20:61289562-61290373 tgaccacaggccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttg gtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgct gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttg @@ -56,9 +56,9 @@ atgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatc caatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgta tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc -gatatccaatgagacttgctggatttatccc----------------------------- ---------------------------------- ->ref_chr20:61289562-61290374 +gatatccaatgagacttgctggatttatcc------------------------------ +-------------------------------- +>ref_chr20:61289562-61290373 tgaccacaggccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttg gtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgct gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttg @@ -72,4 +72,4 @@ caatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgta tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg tatccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttatccc cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc -ccgatatccaatgagacttgctggatttatccc +ccgatatccaatgagacttgctggatttatcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a4fa20a9084e2838ff934c5663169e02.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a4fa20a9084e2838ff934c5663169e02.msa deleted file mode 100644 index 0334106a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a4fa20a9084e2838ff934c5663169e02.msa +++ /dev/null @@ -1,190 +0,0 @@ ->syndip_1_chr20:63948494-63948754 -ccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgagga -gggaggcgtgtgtgagagggaggggatgtgtgtgagaggga-ggggcgtgtgtgagaggg -aggggcgtgtgtgaggg---aggggtgtgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtgtgtgagaggcagggg-gcgtgtgtgtga-ggggcgtgtgtgagagggagggg -cgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtg -tgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagaggg------------- -----aggggcgtgtgtgtgagggaggggcgtgtgagag-ggagggggcgtgtgtgagagg -caggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtgagagggaggggg -cgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgt----gggagggggcgtgt -gtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagacggaggggcgtgtgt -gagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtga -gggagggg---gcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgaga -gggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagaggga -ggggcgtgtgagaggg-aggggcgtgtgtgagagg----------gagggggcgtgtgtg -agagggagggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgaga -gggagggggcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagg -gggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggg -cgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagag--------ggag -ggggcgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagaggga-ggg -gcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggggcgt -gtgtgagagggagggggcgtgt-------------gtgagagggagaggcgtgtgtgaga -gggaggggcgtgtgtgagggagggggcgtgtgtgagagggagaggcgtgtgtgagaggga -gggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggg -gcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggc -gtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg -tgtgagagggag--------------ggggcgtgtgtgagagggaggggcgtgtgtgaga -gggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga-ggggcgtgtgtgagag -ggaggggcgtgtgtgaagggaggggcgtgtgtgagagtgggggcgtgtgtgagttagggg -cgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtg-- ----agagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtg -agagggaaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgag -aggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggg-gcgtgtgagaggga -ggggcgtgtgtgagagggaggggc--gtgtgagagggaggggcgtgtgtgagaggga-gg -ggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgagagggagggggcgtg -tgtgagggaggggcgtgtgtgagagggaggggggcgtgtgtgagagggagggggcgtgtg -tgagagggagggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgag -agggaagcgtgtgcacacaccagccctaacc ->syndip_2_chr20:63948494-63948754 -ccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgagga -gggaggcgtgtgtgagagggaggggatgtgtgtgagagggagggggcgtgtgtgagaggg -aggggcgtgtgtgagag---aggggtgtgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtgtgtgaaagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggagggg -cgtgtgtgagaggcaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtg -tgtgagaggcaggggcgtgtgtgagagtgggggcgtgtgtgagggggggcgtgtgtgaga -gggagggggcgtgtgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagg -gaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgag-gggggggcg -tgtgtgagagggagggggcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgt -gtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtga---agggaggggtgtgt -gtgagagtgggggcgtgtgtgagaggg--------gcgtgagaggtaggggcgtgtgtga -gagggaggggtgtgtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtgag- -ggagggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagaggga -ggggcgtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtgagggggggcgtgtgtg -agaggta-ggggcgtgtgtgagagggaggggcgtgtgtg-agggaggggcgtgtgtgaga -ggcaggggcgtgtgtgggggggggcgtgtgt--gaggggggggcgtgtgtgagagggagg -gggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggg -cgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgaggggggcgtgtgagagg -gaggggcgtgtgtggggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggg -gcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggtgt -gtgtgagagtgggggcgtgtgtgagagttaggggcgtgagaggtaggggcgtgtgtgaga -gggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtgagaggga -gggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagggagggg -gcgtgtgcgagagggaggggcgtgtgtgagagggagggggcgtgtgtgag-ggagggggc -gtgtgtgagagggaggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggggcgtg -tgtgtgagggaggggcgtgagagggaggggcgtgtgtga---gggggggcgtgtgtgaga -ggtaggggcgtgtgtgagagggagggggcgtgtgtgagagggagggggcgtgtgtgagag -ggaggggcgtgtgtgagggagggggcgtgt------------------------------ --gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtg -tgagagggagggggcgtgtgtgagagggaggggcgtgtgtga-agggaggggcgtgtgtg -agagtg--ggggcgtgtgtgagaggg--------gcgtgagaggtaggggcgtgtgtgag -agggagggg-gcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggga -ggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagggaggg -ggcgtgtgtgagagggaggggcgtgt---------------gtgagagggaaggggcgtg -tgagagggaggggcgtgtgtgagaggaaggggcgtgtgtgaga---gggaggggcgtgtg -tgagagggagggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgag -agggaagcgtgtgcacacaccagccctaacc ->p:HG002_1_chr20:63948494-63948754 -ccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgagga -gggaggcgtgtgtgagagggaggggatgtgtgtgagagggagggggcgtgtgtgagaggg -aggggcgtgtgtgagag---aggggtgtgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtgtgtgaaagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggagggg -cgtgtgtgagaggcaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtg -tgtgagaggcaggggcgtgtgtgagagtgggggcgtgtgtgagggggggcgtgtgtgaga -gggagggggcgtgtgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagg -gaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgag-gggggggcg -tgtgtgagagggagggggcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgt -gtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtga---agggaggggtgtgt -gtgagagtgggggcgtgtgtgagaggg--------gcgtgagaggtaggggcgtgtgtga -gagggaggggtgtgtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtgag- -ggagggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagaggga -ggggcgtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtgagggggggcgtgtgtg -agaggta-ggggcgtgtgtgagagggaggggcgtgtgtg-agggaggggcgtgtgtgaga -ggcaggggcgtgtgtgggggggggcgtgtgt--gaggggggggcgtgtgtgagagggagg -gggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggg -cgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgaggggggcgtgtgagagg -gaggggcgtgtgtggggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggg -gcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggtgt -gtgtgagagtgggggcgtgtgtgagagttaggggcgtgagaggtaggggcgtgtgtgaga -gggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtgagaggga -gggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagggagggg -gcgtgtgcgagagggaggggcgtgtgtgagagggagggggcgtgtgtgag-ggagggggc -gtgtgtgagagggaggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggggcgtg -tgtgtgagggaggggcgtgagagggaggggcgtgtgtga---gggggggcgtgtgtgaga -ggtaggggcgtgtgtgagagggagggggcgtgtgtgagagggagggggcgtgtgtgagag -ggaggggcgtgtgtgagggagggggcgtgt------------------------------ --gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtg -tgagagggagggggcgtgtgtgagagggaggggcgtgtgtga-agggaggggcgtgtgtg -agagtg--ggggcgtgtgtgagaggg--------gcgtgagaggtaggggcgtgtgtgag -agggagggg-gcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggga -ggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagggaggg -ggcgtgtgtgagagggaggggcgtgt---------------gtgagagggaaggggcgtg -tgagagggaggggcgtgtgtgagaggaaggggcgtgtgtgaga---gggaggggcgtgtg -tgagagggagggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgag -agggaagcgtgtgcacacaccagccctaacc ->p:HG002_2_chr20:63948494-63948754 -ccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgagga -gggaggcgtgtgtgagagggaggggatgtgtgtgagagggagggggcgtgtgtgagaggg -aggggcgtgtgtgag-----aggggtgtgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtgtgtgagaggcagggg-gcgtgtgtgtga-ggggcgtgtgtgagagggagggg -cgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtg -tgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagaggg------------- -----aggggcgtgtgtgtgagggaggggcgtgtgagag-ggagggggcgtgtgtgagagg -caggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtgagagggaggggg -cgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgt----gggagggggcgtgt -gtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagacggaggggcgtgtgt -gagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtga -gggagggg---gcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgaga -gggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagaggga -ggggcgtgtgagaggg-aggggcgtgtgtgagagg----------gagggggcgtgtgtg -agagggagggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgaga -gggagggggcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagg -gggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggg -cgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagag--------ggag -ggggcgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagaggga-ggg -gcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggggcgt -gtgtgagagggagggggcgtgt-------------gtgagagggagaggcgtgtgtgaga -gggaggggcgtgtgtgagggagggggcgtgtgtgagagggagaggcgtgtgtgagaggga -gggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggg -gcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggc -gtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg -tgtgagagggag--------------ggggcgtgtgtgagagggaggggcgtgtgtgaga -gggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga-ggggcgtgtgtgagag -ggaggggcgtgtgtgaagggaggggcgtgtgtgagagtgggggcgtgtgtgagttagggg -cgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtg-- ----agagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtg -agagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgag -aggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggg-gcgtgtgagaggga -ggggcgtgtgtgagagggaggggc--gtgtgagagggaggggcgtgtgtgagaggga-gg -ggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgagagggagggggcgtg -tgtgaggaaggggcgtgtgtgagagggaggggggcgtgtgtgagagggagggggcgtgtg -tgagagggagggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgag -agggaagcgtgtgcacacaccagccctaacc ->ref_chr20:63948494-63948754 -ccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgagga -gggaggcgtgtgtgagagggaggggatgtgtgtgagagggagggggcgtgtgtgagaggg -aggggcgtgtgtgagagggaaggggcgtgtgtgagagggaggggcgtgtgtgagagggag -ggggtgtgtgtgagaccgagggg-gcgtgtaagggagggggtgtgtgtgagagggaagcg -tgtgcaca---------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------caccagccctaacc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_31498c5319740498de0c72700ff85d56.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a9d398ab39129efb27eabfa2cdf49d07.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_31498c5319740498de0c72700ff85d56.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_a9d398ab39129efb27eabfa2cdf49d07.msa index 8dbb59b0..b50a92ee 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_31498c5319740498de0c72700ff85d56.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_a9d398ab39129efb27eabfa2cdf49d07.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:62349512-62350033 +>syndip_1_chr20:62349512-62350032 gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg @@ -25,8 +25,8 @@ ggtgggggtgggggtgatgacggtgat--------------------------------- ------------------------ggtgggggtgatgatggtgggagtgggctggtagtg ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag -ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc ->syndip_2_chr20:62349512-62350033 +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtc +>syndip_2_chr20:62349512-62350032 gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg @@ -53,8 +53,8 @@ gggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtggg ggtgatggtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctggtagtg ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag -ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc ->p:HG002_1_chr20:62349512-62350033 +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtc +>p:HG002_1_chr20:62349512-62350032 gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg @@ -81,8 +81,8 @@ gggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtggg ggtgatggtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctggtagtg ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag -ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc ->p:HG002_2_chr20:62349512-62350033 +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtc +>p:HG002_2_chr20:62349512-62350032 gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg @@ -109,8 +109,8 @@ ggtgggggtgggggtgatgacggtgat--------------------------------- ------------------------ggtgggggtgatgatggtgggagtgggctggtagtg ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag -ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc ->ref_chr20:62349512-62350033 +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtc +>ref_chr20:62349512-62350032 gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac aattccggatagactgtcatggaatagaaaaactacagggtgcatttcag---------- ------------------------------------------------------------ @@ -137,4 +137,4 @@ ggtgatggtgggggtgatgacggtgat--------------------------------- ------------------------ggtgggggtgatgatggtgggagtgggctggtagtg ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag -ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc +ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_67b17e44da59d4e4cbdbdfe00749d51f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_aaf3284dfcd9e22479f7e2d5c0551083.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_67b17e44da59d4e4cbdbdfe00749d51f.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_aaf3284dfcd9e22479f7e2d5c0551083.msa index 7c44fb6d..b9a35234 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_67b17e44da59d4e4cbdbdfe00749d51f.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_aaf3284dfcd9e22479f7e2d5c0551083.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:22081861-22084223 +>syndip_1_chr20:22081861-22084222 ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt @@ -45,8 +45,8 @@ atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag -aattaaagtaagagttttctttctttcatctcctttttatctctctca ->syndip_2_chr20:22081861-22084223 +aattaaagtaagagttttctttctttcatctcctttttatctctctc +>syndip_2_chr20:22081861-22084222 ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt @@ -93,8 +93,8 @@ atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag -aattaaagtaagagttttctttctttcatctcctttttatctctctca ->p:HG002_1_chr20:22081861-22084223 +aattaaagtaagagttttctttctttcatctcctttttatctctctc +>p:HG002_1_chr20:22081861-22084222 ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt @@ -141,8 +141,8 @@ atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag -aattaaagtaagagttttctttctttcatctcctttttatctctctca ->p:HG002_2_chr20:22081861-22084223 +aattaaagtaagagttttctttctttcatctcctttttatctctctc +>p:HG002_2_chr20:22081861-22084222 ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt @@ -189,8 +189,8 @@ atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag -aattaaagtaagagttttctttctttcatctcctttttatctctctca ->ref_chr20:22081861-22084223 +aattaaagtaagagttttctttctttcatctcctttttatctctctc +>ref_chr20:22081861-22084222 ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt @@ -237,4 +237,4 @@ atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag -aattaaagtaagagttttctttctttcatctcctttttatctctctca +aattaaagtaagagttttctttctttcatctcctttttatctctctc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c7c98c4fca6fe269a9994162cd302ea0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ac49004ec0dccaa0aa222eebaca554b5.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_c7c98c4fca6fe269a9994162cd302ea0.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_ac49004ec0dccaa0aa222eebaca554b5.msa index 02da97d1..360afd32 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c7c98c4fca6fe269a9994162cd302ea0.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_ac49004ec0dccaa0aa222eebaca554b5.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:8661811-8662758 +>syndip_1_chr20:8661811-8662757 gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta @@ -31,8 +31,8 @@ ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat atatattattaacataatatctaaatatattaataatctaatatctataattaatataat atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca -aaggcccacacc ->syndip_2_chr20:8661811-8662758 +aaggcccacac +>syndip_2_chr20:8661811-8662757 gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc tcttaaaagtgtatatatatataattatataattatttattatataatgatatataatta @@ -65,8 +65,8 @@ ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat atatattattaacataatatctaaatatattaataatctaatatctataattaatataat atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca -aaggcccacacc ->p:HG002_1_chr20:8661811-8662758 +aaggcccacac +>p:HG002_1_chr20:8661811-8662757 gccaacctacgttaagtaattcataacttcagtattcaataaatcttcagtgaaaggcaa gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc tcttaaaagtgtatatatatataattatataattatttattatataatgatatataatta @@ -99,8 +99,8 @@ ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat atatattattaacataatatctaaatatattaataatctaatatctataattaatataat atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca -aaggcccacacc ->p:HG002_2_chr20:8661811-8662758 +aaggcccacac +>p:HG002_2_chr20:8661811-8662757 gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta @@ -133,8 +133,8 @@ ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat atatattattaacataatatctaaatatattaataatctaatatctataattaatataat atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca -aaggcccacacc ->ref_chr20:8661811-8662758 +aaggcccacac +>ref_chr20:8661811-8662757 gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc tcttaaaag--------------------------------------------------- @@ -167,4 +167,4 @@ ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat atatattattaacataatatctaaatatattaataatctaatatctataattaatataat atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca -aaggcccacacc +aaggcccacac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ae16a0bdeb31c91e26795edee8ad33fb.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ae16a0bdeb31c91e26795edee8ad33fb.msa deleted file mode 100644 index a5d29a6d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ae16a0bdeb31c91e26795edee8ad33fb.msa +++ /dev/null @@ -1,660 +0,0 @@ ->syndip_1_chr20:63693225-63693985 -tcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactgg -taaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagt -cctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccct -atgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccaccttc -accaccaccacctccaccaccacctccaccacctccacctccaccacctccaccacctcc -accaccaccacctccaccaccaccacctccaccaccaccaccaccaccacctccaccacc -accaccaccaccaccacctccacctccaccacctccaccaccacctccacctccaccacc -acctccacctccacctccaccaccaccacctccaccacctccaccacctccacctccacc -accacctccacctccaccaccacctccacctccacctccacctccacctccaccaccacc -acctccaccacctccaccacctccacctccaccaccaccacctccacctccacctccacc -acctccacctccaccacctccacctccaccacctccaccaccaccaccaccaccaccacc -acctccaccaccaccaccaccaccacctccaccacctccacctccaccacctccaccacc -accacctccaccaccacctccaccaccacctccacctccaccacctccacctccaccacc -tccacctccacctccaccaccacctccaccacctccaccaccacctccaccacctccacc -tccaccaccaccacctccaccaccaccaccaccaccacctccaccacctccacctccacc -acctccaccaccaccacctccaccaccacctccaccaccacctccacctccaccacctcc -acctccaccacctccacctccacctccaccaccacctccaccacctccaccaccacctcc -accacctccaccacctccaccaccacctccaccacctccacctccaccaccaccacctcc -acctccaccaccaccacctccaccaccacctccacctccaccaccaccacctccacctcc -accaccaccacctccacca---ccacctccaccaccaccaccaccaccaccacctccacc -tccaccacctccaccaccaccaccaccacctccacctccaccacctccaccacctccacc -accaccaccaccacctccaccacctccaccaccacctccaccacctccacctccaccacc -accacctccaccaccaccacctccacctccacctccacctccacctccaccaccacctcc -acctccaccaccacctccaccaccacctccacctccaccacctccacctccacctccacc -acctccaccaccaccaccaccaccaccaccaccaccaccacctccaccacctccacctcc -acctccaccaccaccaccaccacctccaccaccaccaccaccacctccaccacctccacc -accacctccaccaccaccaccaccaccaccaccaccacctccaccacctccacctccacc -tccacctccaccacctccaccacctccaccaccacctccaccaccaccaccaccacctcc -accaccacctccacctccaccaccacctccaccaccacctccacctccaccacctccacc -tccaccacctccaccacctccacctccaccacctccacctccacctccaccacctccacc -accaccaccaccaccaccaccaccaccaccacctccaccaccaccacctccaccaccacc -tccaccacctccaccaccacctccaccaccaccaccaccaccaccaccaccaccaccacc -tccaccaccacctccacctccaccaccacctccaccaccacctccacctccaccacctcc -acctccaccacctccaccacctccaccaccaccaccaccacctccaccaccacctccacc -tccaccaccaccaccaccaccaccacctccaccaccaccacctccaccaccacctccacc -acctccaccaccacctccacctccaccacctccaccaccacctccaccaccacctccacc -accaccacctccaccaccacctccaccacctccaccaccacctccacctccaccacctcc 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-acctccaccaccacctccacctccaccaccacctcctccaccaccaccacctccaccacc -acctccaccaccaccacctccacctccaccacctccacctccaccaccaccacctccacc -tccaccaccaccacctccaccacctccaccaccacctccaccacctccacctccaccacc -accacctccaccaccaccacctccacctccaccaccaccaccaccaccacctccacctcc -accaccacctccaccaccacctccacctccacctccaccacctccaccaccacctccacc -acctccaccacctccacctccaccaccaccaccacctccaccaccaccaccaccacctct -accacctctaccaccaccaccaccacctccaccaccaccaccaccacctccaccaccacc -accaccaccacctccaccaccacctccaccacctccaccaccaccaccaccacctctacc -acctccacctccaccaccaccaccacctctaccaccaccaccaccacctccaccaccacc -accacctccaccaccaccaccacctccaccaccacctccaccaccacctccaccacctcc -accaccaccaccacctccacctccaccacctccaccaccacctccaccaccaccaccacc -accacctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctcc -acctccaccaccaccaccacctccacctccaccaccaccaccaccaccaccaccaccacc -acctccaccaccaccaccaccaccacctctaccaccaccaccaccacctccaccaccacc -accacctccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccacc -accacctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccaccacc -acctccaccaccacctccaccaccaccaccacctccaccaccacctccaccaccacctcc -accacctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccacc -accacctccaccaccaccaccaccaccaccacctccaccaccacctccaccaccacctcc -accacctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccacc -accacctccaccaccacctccaccaccaccaccaccaccacctccaccaccacctccacc -acctccaccaccaccaccaccacctctaccacctctaccaccaccaccaccacctccacc -accaccaccacctccaccaccaccaccacctccaccaccaccacctccacctccaccacc -accacctccaccacctccaccaccacctccaccaccaccacctccacctccaccaccacc -acctccaccacctccaccaccaccaccaccaccaccaccacctccaccaccaccaccacc -accacctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctct -accaccaccaccaccacctccaccaccaccaccacctccaccaccaccaccacctccacc -accacctccaccaccaccacctccacctccaccaccaccacctccaccaccaccacctcc -acctccaccaccaccacctccaccacctccaccaccacctccaccaccaccacctccacc -tccaccaccaccacctccaccacctccaccaccaccacctccaccaccaccacctccacc -acctccaccaccaccaccaccacctccaccacctccaccacctccaccaccaccaccacc -acctccacctccacctccaccacctccaccaccaccacctccaccaccaccaccaccacc 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-tccaccacctccacctccacctccaccacctccaccaccaccaccaccaccaccaccacc -accaccacctccaccaccaccacctccaccaccacctccaccaccaccaccaccacctcc -accaccaccaccaccacctccaccaccacctccaccacctccaccaccaccaccaccacc -accaccacctccaccaccacctccaccaccaccaccaccaccaccaccacctccaccacc -tccacctccaccaccaccaccacctccaccaccaccaccaccaccacctccacctccacc -accaccacctccaccaccaccaccacctccaccaccacctccaccaccaccaccaccacc -accaccaccacctccaccacctccaccacctccaccaccacctccaccacctccaccacc -accaccaccacctccaccaccacctccaccaccaccaccaccaccaccacctccacctcc -acctccaccacctccacctccaccacctccacctccaccacctccacctccacctccacc -acctccaccaccacctccacctccaccaccacctcctccaccaccaccacctccaccacc -acctccaccaccaccacctccacctccaccacctccacctccaccaccaccacctccacc -tccaccaccaccacctccaccacctccaccaccacctccaccacctccacctccaccacc -accacctccaccaccaccacctccacctccaccaccaccaccaccaccacctccacctcc -accaccacctccaccaccacctccacctccacctccaccacctccaccaccacctccacc -acctccaccacctccacctccaccaccaccaccacctccaccaccaccaccaccacctct -accacctctaccaccaccaccaccacctccaccaccaccaccaccacctccaccaccacc -accaccaccacctccaccaccacctccaccacctccaccaccaccaccaccacctctacc -acctccacctccaccaccaccaccacctctaccaccaccaccaccacctccaccaccacc -accacctccaccaccaccaccacctccaccaccacctccaccaccacctccaccacctcc -accaccaccaccacctccacctccaccacctccaccaccacctccaccaccaccaccacc -accacctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctcc -acctccaccaccaccaccacctccacctccaccaccaccaccaccaccaccaccaccacc -acctccaccaccaccaccaccaccacctctaccaccaccaccaccacctccaccaccacc -accacctccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccacc -accacctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccaccacc -acctccaccaccacctccaccaccaccaccacctccaccaccacctccaccaccacctcc -accacctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccacc -accacctccaccaccaccaccaccaccaccacctccaccaccacctccaccaccacctcc -accacctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccacc -accacctccaccaccacctccaccaccaccaccaccaccacctccaccaccacctccacc -acctccaccaccaccaccaccacctctaccacctctaccaccaccaccaccacctccacc -accaccaccacctccaccaccaccaccacctccaccaccaccacctccacctccaccacc -accacctccaccacctccaccaccacctccaccaccaccacctccacctccaccaccacc -acctccaccacctccaccaccaccaccaccaccaccaccacctccaccaccaccaccacc -accacctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctct -accaccaccaccaccacctccaccaccaccaccacctccaccaccaccaccacctccacc -accacctccaccaccaccacctccacctccaccaccaccacctccaccaccaccacctcc -acctccaccaccaccacctccaccacctccaccaccacctccaccaccaccacctccacc -tccaccaccaccacctccaccacctccaccaccaccacctccaccaccaccacctccacc -acctccaccaccaccaccaccacctccaccacctccaccacctccaccaccaccaccacc -acctccacctccacctccaccacctccaccaccaccacctccaccaccaccaccaccacc -accaccacctccacctccacctccaccacctccacctccaccaccaccaccaccaccacc -accaccaccaccacctccacctccacctccaccacctccaccaccaccacctccaccacc -accacctccacctccaccacctccaccaccacctccaccaccaccacctccacctccacc -accaccacctccaccaccaccacctccacctccaccaccaccacctccaccacctccacc -accacctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccacc -accacctccaccaccaccacctccaccacctccaccaccaccaccaccacctccaccacc -tccaccacctccaccaccaccaccaccacctccacctccacctccaccacctccaccacc -accacctccaccaccaccaccaccaccacctccaccacctccaccaccaccaccaccacc -tccacctccacctccaccacctccaccaccaccacctccaccaccaccaccaccaccacc -accaccacctccacctccacctccaccacctccacctccaccaccaccaccaccaccacc -acctccaccaccacctccacctccacctccaccacctccacctccaccaccaccaccacc -accaccaccaccaccaccacctccacctccacctccaccaccaccacctctaccaccacc -tccaccaccaccaccaccaccaccaccaccacctccaccacctccaccaccaccacctcc -accaccaccacctccacctccaccaccaccaccacctccaccacctccaccaccacctcc -acctccacctccaccacctccaccaccaccacctccaccaccaccaccaccaccaccacc -tccaccacctccaccaccaccacctccaccaccaccacctccacctccaccacctccacc -acctccaccaccaccaccacctccaccaccaccaccaccaccacctccacctccaccacc -tctaccaccacctccaccaccaccaccaccaccacctccacctccaccacctccacctcc -accacctctaccaccacctccaccaccaccacctccacctccacctccaccaccaccacc -tccacctccacctccaccaccaccaccaccaccaccacctccaccaccaccaccaccacc -accaccaccacctccacctccaccaccaccacctccaccaccaccacctccaccacctcc -accaccacctccacctccaccaccaccacctccacctccacctccaccaccaccaccacc -acctccaccaccaccacctccaccaccaacacctccacctccacctccaccaccaccacc -accacctccacctccaccaccacctccaccaccaccacctccacctccaccaccaccacc -tccaccaccacctccaccacctccaccaccaccacctccaccaccacctccaccaccacc -accaccaccacctccacctccacctccaccaccaccacctctaccaccacctccaccacc -accaccaccaccaccaccaccacctccacctccacctccaccacctccacctccaccacc -accaccaccaccaccacctccaccaccacctccacctccacctccaccacctccacctcc -accaccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccaccacc -acctctaccaccacctccaccaccaccaccaccaccaccaccaccacctccaccaccacc -acctccacctccaccaccaccacctccacctccaccaccaccacctccacctccaccacc -accaccaccaccaccacctccaccaccaccacctccaccacctccaccaccacctccacc -accaccacctccaccacctccaccaccacctccacctccaccaccaccacctccaccacc -accacctccacctccaccaccaccacctccacctccacctccaccacctccacctccacc -acctccaccaccaccacctccaccacctccaccaccacctccacctccaccaccaccacc -tccaccaccaccacctccaccacctccaccaccacctccacctccaccaccaccacctcc -acctccacctccaccaccaccaccaccacctccactaccaccacctccacctccaccacc -accacctccaccaccaacacctccacctccacctccacctccaccaccaccacctccacc -tccaccaccaccacctccaccaccaccacctccaccacctccacctccaccaccaccacc -tccaccaccacctccaccaccaccaccacctccaccaccaccacctccaccaccacctcc -accaccaccacctccaccaccacctccaccaccacctccacctccaccaccaccacctgc -accaccacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcact -tgttggggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgacccc -taagcacagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctgggggg -tcaactgcacacgccagggtcctagggtcctagacccctgtcctccctgtttctgcctct -gtttggggtggagtccaagtctc ->ref_chr20:63693225-63693985 -tcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactgg -taaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagt -cctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccct -atgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacct-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- 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------------------------------------------------------------- -----------------------ccacctccacct-------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------------cc -acctccaccaccacctccacctccaccaccacctcctccaccaccaccacctccaccacc -accaccaccaccaccacctccacctccaccacctccacctccaccaccaccacctccacc -t----------------------------------------------------------- ------------------------------------------------------------- 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------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------ccaccacc -accacctccacctccaccaccacctccaccaccaccacctccacctccacca-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------ccacctcc -accaccaccaccaccaccaccaccaccaccacca-------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------ccacctccaccaccaccacctgc -accaccacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcact -tgttggggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgacccc -taagcacagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctgggggg -tcaactgcacacgccagggtcctagggtcctagacccctgtcctccctgtttctgcctct -gtttggggtggagtccaagtctc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_21e1c5c85ccc2580c7576396ab027d39.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ae89171a433f770e25870ba2623263b5.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_21e1c5c85ccc2580c7576396ab027d39.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_ae89171a433f770e25870ba2623263b5.msa index ecf894da..15777a46 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_21e1c5c85ccc2580c7576396ab027d39.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_ae89171a433f770e25870ba2623263b5.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:48449605-48450562 +>syndip_1_chr20:48449605-48450561 catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg @@ -23,8 +23,8 @@ tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg -gacaaagcacttaaaaccacacagt ->syndip_2_chr20:48449605-48450562 +gacaaagcacttaaaaccacacag +>syndip_2_chr20:48449605-48450561 catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg @@ -49,8 +49,8 @@ tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga ttggatggggtgggatgcgatgggatgagatgagatgagatgaatggcatgggatgggtg ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg -gacaaagcacttaaaaccacacagt ->p:HG002_1_chr20:48449605-48450562 +gacaaagcacttaaaaccacacag +>p:HG002_1_chr20:48449605-48450561 catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg @@ -75,8 +75,8 @@ tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga ttggatggggtgggatgcgatgggatgagatgagatgagatgaatggcatgggatgggtg ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg -gacaaagcacttaaaaccacacagt ->p:HG002_2_chr20:48449605-48450562 +gacaaagcacttaaaaccacacag +>p:HG002_2_chr20:48449605-48450561 catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg @@ -101,8 +101,8 @@ tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg -gacaaagcacttaaaaccacacagt ->ref_chr20:48449605-48450562 +gacaaagcacttaaaaccacacag +>ref_chr20:48449605-48450561 catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg @@ -127,4 +127,4 @@ tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg -gacaaagcacttaaaaccacacagt +gacaaagcacttaaaaccacacag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9977644ffc467b937358e85a6ba26103.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b05e3a291363048d6af177602ce2b043.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_9977644ffc467b937358e85a6ba26103.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_b05e3a291363048d6af177602ce2b043.msa index 285703c8..40bd6c04 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9977644ffc467b937358e85a6ba26103.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_b05e3a291363048d6af177602ce2b043.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:14861837-14862842 +>syndip_1_chr20:14861837-14862841 gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac attggaggttttatatataaatatatatatatatttatatatatatttatatatatatat @@ -28,8 +28,8 @@ aaatatatatataaatataaatatatatgtataaatatatatataaatatatatatataa atatatatatacatatataaatatatatataaatatatataaaaatatatatatatatat ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca -gaag ->syndip_2_chr20:14861837-14862842 +gaa +>syndip_2_chr20:14861837-14862841 gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat @@ -59,8 +59,8 @@ aaatatatatataaatatatataaatatatataaaaatatatataaatatatatataaat atatatataaatatatataaatatatatataaatatatataaaaatatatatatattttt ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca -gaag ->p:HG002_1_chr20:14861837-14862842 +gaa +>p:HG002_1_chr20:14861837-14862841 gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat @@ -90,8 +90,8 @@ aaatatatatataaatatatataaatatatataaaaatatatataaatatatatataaat atatatataaatatatataaatatatatataaatatatataaaaatatatatatattttt ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca -gaag ->p:HG002_2_chr20:14861837-14862842 +gaa +>p:HG002_2_chr20:14861837-14862841 gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac attggaggttttatatataaatatatatatatatttatatatatatttatatatatatat @@ -121,8 +121,8 @@ aaatatatatataaatataaatatatatgtataaatatatatataaatatatatatataa atatatatatacatatataaatatatatataaatatatataaaaatatatatatatatat ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca -gaag ->ref_chr20:14861837-14862842 +gaa +>ref_chr20:14861837-14862841 gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat @@ -152,4 +152,4 @@ aaatatatatataaat------------------------------atatatatataaat atatatataaatatatataaatatatatataaatatatataaatatatatatatatattt ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca -gaag +gaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c3e3f9602fee97132e713a8085d0122f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b179a5501273075e792cbf44d023019b.msa similarity index 98% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_c3e3f9602fee97132e713a8085d0122f.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_b179a5501273075e792cbf44d023019b.msa index eda44657..0b5b5c0f 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c3e3f9602fee97132e713a8085d0122f.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_b179a5501273075e792cbf44d023019b.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:38462831-38464884 +>syndip_1_chr20:38462831-38464883 caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat @@ -67,8 +67,8 @@ agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc -cagcctgggcaacagagcaagactctgtctccaaaaaaa- ->syndip_2_chr20:38462831-38464884 +cagcctgggcaacagagcaagactctgtctccaaaaaa- +>syndip_2_chr20:38462831-38464883 caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat @@ -137,8 +137,8 @@ agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc -cagcctgggcaacagagcaagactctgtctccaaaaaaaa ->p:HG002_1_chr20:38462831-38464884 +cagcctgggcaacagagcaagactctgtctccaaaaaaa +>p:HG002_1_chr20:38462831-38464883 caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat @@ -207,8 +207,8 @@ agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc -cagcctgggcaacagagcaagactctgtctccaaaaaaaa ->p:HG002_2_chr20:38462831-38464884 +cagcctgggcaacagagcaagactctgtctccaaaaaaa +>p:HG002_2_chr20:38462831-38464883 caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat @@ -277,8 +277,8 @@ agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc -cagcctgggcaacagagcaagactctgtctccaaaaaaa- ->ref_chr20:38462831-38464884 +cagcctgggcaacagagcaagactctgtctccaaaaaa- +>ref_chr20:38462831-38464883 caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat @@ -347,4 +347,4 @@ agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc -cagcctgggcaacagagcaagactctgtctccaaaaaaa- +cagcctgggcaacagagcaagactctgtctccaaaaaa- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4abdcd3bd686c6653b94c23219e870d1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b206928da83df6d728521bb51cfc7a4d.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_4abdcd3bd686c6653b94c23219e870d1.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_b206928da83df6d728521bb51cfc7a4d.msa index 5f9abff0..29d71e41 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4abdcd3bd686c6653b94c23219e870d1.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_b206928da83df6d728521bb51cfc7a4d.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:4032119-4033702 +>syndip_1_chr20:4032119-4033701 cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag cggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaaa gagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctct @@ -31,8 +31,8 @@ agtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttc tgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgg gaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaat agaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtgg -atggaagtagacatg ->syndip_2_chr20:4032119-4033702 +atggaagtagacat +>syndip_2_chr20:4032119-4033701 cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag cggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaaa gagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctct @@ -65,8 +65,8 @@ agtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttc tgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgg gaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaat agaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtgg -atggaagtagacatg ->p:HG002_1_chr20:4032119-4033702 +atggaagtagacat +>p:HG002_1_chr20:4032119-4033701 cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag cggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaaa gagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctct @@ -99,8 +99,8 @@ agtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttc tgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgg gaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaat agaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtgg -atggaagtagacatg ->p:HG002_2_chr20:4032119-4033702 +atggaagtagacat +>p:HG002_2_chr20:4032119-4033701 cgggattgcagatgaagtctcgttcactcagtgctcaatggtgcccaggctggagtgcag tggcgtgatctccgctcgctacaacctccacctcccagccgcctgccttggcctcccaaa gagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctct @@ -133,8 +133,8 @@ agtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttc tgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgg gaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaat agaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtgg -atggaagtagacatg ->ref_chr20:4032119-4033702 +atggaagtagacat +>ref_chr20:4032119-4033701 cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag cggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaaa gagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctct @@ -167,4 +167,4 @@ agtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttc tgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgg gaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaat agaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtgg -atggaagtagacatg +atggaagtagacat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ef7cdfd52679d33bb0bc51f849df45e1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b4b25fe75fa812465ce27c19d1fe0ff9.msa similarity index 98% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_ef7cdfd52679d33bb0bc51f849df45e1.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_b4b25fe75fa812465ce27c19d1fe0ff9.msa index 6107bb73..2b529a23 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ef7cdfd52679d33bb0bc51f849df45e1.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_b4b25fe75fa812465ce27c19d1fe0ff9.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:56280322-56282215 +>syndip_1_chr20:56280322-56282214 ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa @@ -42,8 +42,8 @@ tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt -cttatccct ->syndip_2_chr20:56280322-56282215 +cttatccc +>syndip_2_chr20:56280322-56282214 ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa @@ -87,8 +87,8 @@ tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt -cttatccct ->p:HG002_1_chr20:56280322-56282215 +cttatccc +>p:HG002_1_chr20:56280322-56282214 ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa @@ -132,8 +132,8 @@ tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt -cttatccct ->p:HG002_2_chr20:56280322-56282215 +cttatccc +>p:HG002_2_chr20:56280322-56282214 ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa @@ -177,8 +177,8 @@ tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt actctcgatactgggacacttttaatcattgctataatacattaattttaatctaatctt -cttatccct ->ref_chr20:56280322-56282215 +cttatccc +>ref_chr20:56280322-56282214 ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa @@ -222,4 +222,4 @@ tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt -cttatccct +cttatccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_dbde05d75f12d66b45769c5ffa50cc28.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b592bd7606102ee30703461d14728bdd.msa similarity index 93% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_dbde05d75f12d66b45769c5ffa50cc28.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_b592bd7606102ee30703461d14728bdd.msa index 9af4c6cc..82b0e36d 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_dbde05d75f12d66b45769c5ffa50cc28.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_b592bd7606102ee30703461d14728bdd.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:2240825-2241827 +>syndip_1_chr20:2240825-2241826 gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt @@ -16,8 +16,8 @@ ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc -tttgcagtttaccagattcacttatgtacattctc ->syndip_2_chr20:2240825-2241827 +tttgcagtttaccagattcacttatgtacattct +>syndip_2_chr20:2240825-2241826 gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat cttctcaaagttttctt-------------------tttctttctttctttttctttctt @@ -35,8 +35,8 @@ ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc -tttgcagtttaccagattcacttatgtacattctc ->p:HG002_1_chr20:2240825-2241827 +tttgcagtttaccagattcacttatgtacattct +>p:HG002_1_chr20:2240825-2241826 gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat cttctcaaagttttctt-------------------tttctttctttctttttctttctt @@ -54,8 +54,8 @@ ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg gtcttgctatgttccccaggctagtctcaaactcctgggctcaagtgatcctccagcctc agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc -tttgcagtttaccagattcacttatgtacattctc ->p:HG002_2_chr20:2240825-2241827 +tttgcagtttaccagattcacttatgtacattct +>p:HG002_2_chr20:2240825-2241826 gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt @@ -73,8 +73,8 @@ ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc -tttgcagtttaccagattcacttatgtacattctc ->ref_chr20:2240825-2241827 +tttgcagtttaccagattcacttatgtacattct +>ref_chr20:2240825-2241826 gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt @@ -92,4 +92,4 @@ ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc -tttgcagtttaccagattcacttatgtacattctc +tttgcagtttaccagattcacttatgtacattct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_cc4f07f5b329711758a6a183602ba892.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b8963eabf50fbefd5fbf150779abc34d.msa similarity index 93% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_cc4f07f5b329711758a6a183602ba892.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_b8963eabf50fbefd5fbf150779abc34d.msa index a3c838e8..c9333764 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_cc4f07f5b329711758a6a183602ba892.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_b8963eabf50fbefd5fbf150779abc34d.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:57189846-57190641 +>syndip_1_chr20:57189846-57190640 ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc @@ -12,8 +12,8 @@ gtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggc tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc -gtgtggggaaccaacaaggc ->syndip_2_chr20:57189846-57190641 +gtgtggggaaccaacaagg +>syndip_2_chr20:57189846-57190640 ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc @@ -27,8 +27,8 @@ aaggggtgaggctggagacagtgagcgaggaacca------------------------- tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc -gtgtggggaaccaacaaggc ->p:HG002_1_chr20:57189846-57190641 +gtgtggggaaccaacaagg +>p:HG002_1_chr20:57189846-57190640 ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta cagggcagagtgagccatgggaggctttggggaggaaatgttcctggcagagggaatggc @@ -42,8 +42,8 @@ aaggggtgaggctggagacagtgagcgaggaacca------------------------- tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc -gtgtggggaaccaacaaggc ->p:HG002_2_chr20:57189846-57190641 +gtgtggggaaccaacaagg +>p:HG002_2_chr20:57189846-57190640 ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta cagggcagagtgagccatgggaggctttggggaggaaatgttcctggcagagggaatggc @@ -57,8 +57,8 @@ gtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggc tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc -gtgtggggaaccaacaaggc ->ref_chr20:57189846-57190641 +gtgtggggaaccaacaagg +>ref_chr20:57189846-57190640 ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc @@ -72,4 +72,4 @@ gtgaggagcccgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc -gtgtggggaaccaacaaggc +gtgtggggaaccaacaagg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0dad6d58073d73f50143dbc812c12c48.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bb633e8a0fe19e3e0ef87827050edb6d.msa similarity index 98% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_0dad6d58073d73f50143dbc812c12c48.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_bb633e8a0fe19e3e0ef87827050edb6d.msa index db18f85a..5353344b 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0dad6d58073d73f50143dbc812c12c48.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_bb633e8a0fe19e3e0ef87827050edb6d.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:64125009-64128075 +>syndip_1_chr20:64125009-64128074 attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt @@ -53,8 +53,8 @@ tacactgtcttgattactac---------------------------------------- atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct -tgc ->syndip_2_chr20:64125009-64128075 +tg +>syndip_2_chr20:64125009-64128074 attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt @@ -109,8 +109,8 @@ cacactgtcttgattactac---------------------------------------- atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct -tgc ->p:HG002_1_chr20:64125009-64128075 +tg +>p:HG002_1_chr20:64125009-64128074 attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt @@ -165,8 +165,8 @@ cacactgtcttgattactac---------------------------------------- atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct -tgc ->p:HG002_2_chr20:64125009-64128075 +tg +>p:HG002_2_chr20:64125009-64128074 attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt @@ -221,8 +221,8 @@ tacactgtcttgattactac---------------------------------------- atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct -tgc ->ref_chr20:64125009-64128075 +tg +>ref_chr20:64125009-64128074 attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt @@ -277,4 +277,4 @@ atactacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct -tgc +tg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_80443f0aed254f4a2d537e2b754a9a7c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bb7fd33627eeebb611fd58a76e4c129f.msa similarity index 88% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_80443f0aed254f4a2d537e2b754a9a7c.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_bb7fd33627eeebb611fd58a76e4c129f.msa index 26e8b92e..92f76260 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_80443f0aed254f4a2d537e2b754a9a7c.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_bb7fd33627eeebb611fd58a76e4c129f.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:61562009-61562353 +>syndip_1_chr20:61562009-61562352 ctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctcccggagaga gagaggggcctccgtgtggagaggtggaccccagggctcccggagagagggacttccgtg tggagaggtggaccccagggctcccggagagagagagggacctccctgagagagagaggg @@ -7,8 +7,8 @@ agaggtggaccccagggctcccagagagagagagggaccttcgtgtggagaggtggaccc cagggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctcccgg agagagagagggacctccgtgtggagaggtggaccccagggctcccg--gagagagggac ctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctgtgtggag -aggtggaccccagggctcccggagagagag ->syndip_2_chr20:61562009-61562353 +aggtggaccccagggctcccggagagaga +>syndip_2_chr20:61562009-61562352 ctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctcccggagaga gagaggggcctccgtgtggagaggtggaccccagggctcccggagagagggacctccgtg tggagaggtggaccccagggctcccggagagagagagggacctccc-------------- @@ -17,8 +17,8 @@ tggagaggtggaccccagggctcccggagagagagagggacctccc-------------- -------------------------------tgtggagaggtggaccccagggctcccag agagagagagggaccttcgtgtggagaggtggaccccagggctcccggagagagagggac ctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctgtgtggag -aggtggaccccagggctcccggagagagag ->p:HG002_1_chr20:61562009-61562353 +aggtggaccccagggctcccggagagaga +>p:HG002_1_chr20:61562009-61562352 ctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctcccggagaga gagaggggcctccgtgtggagaggtggaccccagggctcccggagagagggacctccgtg tggagaggtggaccccagggctcccggagagagagagggacctccc-------------- @@ -27,8 +27,8 @@ tggagaggtggaccccagggctcccggagagagagagggacctccc-------------- -------------------------------tgtggagaggtggaccccagggctcccag agagagagagggaccttcgtgtggagaggtggaccccagggctcccggagagagagggac ctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctgtgtggag -aggtggaccccagggctcccggagagagag ->p:HG002_2_chr20:61562009-61562353 +aggtggaccccagggctcccggagagaga +>p:HG002_2_chr20:61562009-61562352 ctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctcccggagaga gagaggggcctccgtgtggagaggtggaccccagggctcccggagagagggacctccgtg tggagaggtggaccccagggctcccggagagagagagggacctccctgagagagagaggg @@ -37,8 +37,8 @@ agaggtggaccccagggctcccagagagagagagggaccttcgtgtggagaggtggaccc cagggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctcccag agagagagagggaccttcgtgtggagaggtggaccccagggctcccggagagagagggac ctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctgtgtggag -aggtggaccccagggctcccggagagagag ->ref_chr20:61562009-61562353 +aggtggaccccagggctcccggagagaga +>ref_chr20:61562009-61562352 ctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctcccggagaga gagaggggcctccgtgtggagaggtggaccccagggctcccggagagagggacctccgtg tggagaggtggaccccagggctcccggagagagagagggacctccc-------------- @@ -47,4 +47,4 @@ tggagaggtggaccccagggctcccggagagagagagggacctccc-------------- -------------------------------tgtggagaggtggaccccagggctcccag agagagagagggaccttcgtgtggagaggtggaccccagggctcccggagagagagggac ctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctgtgtggag -aggtggaccccagggctcccggagagagag +aggtggaccccagggctcccggagagaga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bbc70dbaa5d67ccdda8d60a17b075dca.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bbc70dbaa5d67ccdda8d60a17b075dca.msa new file mode 100644 index 00000000..94768ca5 --- /dev/null +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_bbc70dbaa5d67ccdda8d60a17b075dca.msa @@ -0,0 +1,295 @@ +>syndip_1_chr20:62057473-62059239 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac +acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg +gacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga +cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca +ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca +ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag +gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca +gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta +cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac +ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag +acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa +tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc +aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac +aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca +ggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacc +tcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggc +tcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga +cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag +acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa +tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac +caggccacagacagtggggctcggggggccaacctcagcaagacctcaggaaggacggac +acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc +aggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaac +ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg +ctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc +cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt +ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa +ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga +caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca +caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg +acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc +tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa +cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg +gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg +ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacg------------------------------------------------------ +-------------------gacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga +caatggggctc------------------------------------------------- +------------------------ggggggccaacctctccagtccccaaacacagtccc +caacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccctc +acacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagct +gggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggca +ggcctggagaagagcctgggaccaccgcggactgac +>syndip_2_chr20:62057473-62059239 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctc------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------ggggg +ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa +tggggctcgggggccaacctca-------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------gcaagacc +tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa +cctcagcaagacctcaggaaggacggacacaggt-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +--ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga +caatggggctc------------------------------------------------- +-------------------------gggggccaacctctccagtccccaaacacagtccc +caacagacaacttctcctgtcctcacatgcggctcccaacaaacaatttctcctgccctc +acacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagct +gggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggca +ggcctggagaagagcctgggaccaccgcggactgac +>p:HG002_1_chr20:62057473-62059239 +tccaagatccatgtaccccaacaccaccctacctggccacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctc------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------ggggg +ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa +tggggctcgggggccaacctca-------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------gcaagacc +tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa +cctcagcaagacctcaggaaggacggacacaggt-------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +--ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga +caatggggctc------------------------------------------------- +-------------------------gggggccaacctctccagtccccaaacacagtccc +caacagacaacttctcctgtcctcacatgcggctcccaacaaacaatttctcctgccctc +acacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagct +gggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggca +ggcctggagaagagcctgggaccaccgcggactgac +>p:HG002_2_chr20:62057473-62059239 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac +acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg +gacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga +cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca +ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca +ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag +gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca +gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta +cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac +ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag +acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa +tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc +aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac +aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca +ggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacc +tcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggc +tcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca +cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct +acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga +cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag +acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa +tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac +caggccacagacagtggggctcggggggccaacctcagcaagacctcaggaaggacggac +acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc +aggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaac +ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg +ctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc +cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt +ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa +ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag +caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga +caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca +caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg +acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc +tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa +cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg +gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg +ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag +gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacg------------------------------------------------------ +-------------------gacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga +caatggggctc------------------------------------------------- +------------------------ggggggccaacctctccagtccccaaacacagtccc +caacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccctc +acacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagct +gggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggca +ggcctggagaagagcctgggaccaccgcggactgac +>ref_chr20:62057473-62059239 +tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag +atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga +cacaaagggcccagcaagacctcaggaaggacggacacaggcctacacaccaggccacag +acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctac +acaccaggccacagacaatggggctcg--------------------------------- +------------------------------------------------------------ +-----------------------------------------------------gggggcc +aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg +gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca +ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca +ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag +gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc +agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc +gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca +gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta +cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac +ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag +acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg +ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa +tggggctcgggggccaacctca-------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------gcaagacc +tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa +cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg +gctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccagg +ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag +gcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga +aggacg------------------------------------------------------ +-------------------gacacaggtctacacaccaggccacagacaatggggctcgg +gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga +caatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacac +accaggccacagacaatggggctcggggggccaacctctccagtccccaaacacagtccc +caacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccctc +acacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagct +gggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggca +ggcctggagaagagcctgggaccaccgcggactgac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b1f9512148e344cd8be442d0b872be80.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bd402172ece6674cf9fbe88768975d74.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_b1f9512148e344cd8be442d0b872be80.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_bd402172ece6674cf9fbe88768975d74.msa index 359a8d58..32620fa1 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b1f9512148e344cd8be442d0b872be80.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_bd402172ece6674cf9fbe88768975d74.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:64173309-64176630 +>syndip_1_chr20:64173309-64176629 cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc @@ -68,8 +68,8 @@ gtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt -------------------ccatttcccctccctggcttctcctgcagcatctttccctg tagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctgg tagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggtg -tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagga ->syndip_2_chr20:64173309-64176630 +tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagg +>syndip_2_chr20:64173309-64176629 cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc @@ -139,8 +139,8 @@ gtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt -------------------ccatttcccctccctggcttctcctgcagcatctttccctg tagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctgg tagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggtg -tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagga ->p:HG002_1_chr20:64173309-64176630 +tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagg +>p:HG002_1_chr20:64173309-64176629 cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc @@ -210,8 +210,8 @@ gtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt -------------------ccatttcccctccctggcttctcctgcagcatctttccctg tagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctgg tagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggtg -tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagga ->p:HG002_2_chr20:64173309-64176630 +tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagg +>p:HG002_2_chr20:64173309-64176629 cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc @@ -281,8 +281,8 @@ gtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt -------------------ccatttcccctccctggcttctcctgcagcatctttccctg tagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctgg tagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggtg -tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagga ->ref_chr20:64173309-64176630 +tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagg +>ref_chr20:64173309-64176629 cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc @@ -352,4 +352,4 @@ tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca tctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg tagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctgg tagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggtg -tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagga +tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_16e133fb197adcc9bd932887b742868b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c00504a27ac55beec570218a4eedf56f.msa similarity index 83% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_16e133fb197adcc9bd932887b742868b.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_c00504a27ac55beec570218a4eedf56f.msa index cb9e5d5b..9a20f373 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_16e133fb197adcc9bd932887b742868b.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_c00504a27ac55beec570218a4eedf56f.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:60702842-60703216 +>syndip_1_chr20:60702842-60703215 tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac atttgtcattgtctttctttcttttctttctctctctctctttcttttccttctttcttt @@ -6,8 +6,8 @@ ctttctttctttctttctttctttctttctttctttctttctttcttttctttccttctt ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt ctttctttctttctttcttctttctttctttttctttcttttttttttgggatggagtct cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct -cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg ->syndip_2_chr20:60702842-60703216 +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagct +>syndip_2_chr20:60702842-60703215 tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac atttgtcattgtctttctttcttttctttctctctctctctctctttcttttccttcttt @@ -15,8 +15,8 @@ ctttctttctttctttctttcttcctttctttctttctttctttctttctttctttcttt ctttct---tttctttccttctttctttctttctttc----------------------- ---------------------------------------tttttttttgggatggagtct cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct -cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg ->p:HG002_1_chr20:60702842-60703216 +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagct +>p:HG002_1_chr20:60702842-60703215 tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac atttgtcattgtctttctttcttttctttctctctctctctctctttcttttccttcttt @@ -24,8 +24,8 @@ ctttctttctttctttctttcttcctttctttctttctttctttctttctttctttcttt ctttct---tttctttccttctttctttctttctttc----------------------- ---------------------------------------tttttttttgggatggagtct cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaacctccacct -cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg ->p:HG002_2_chr20:60702842-60703216 +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagct +>p:HG002_2_chr20:60702842-60703215 tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac atttgtcattgtctttctttcttttctttctctctctctctttcttttccttctttcttt @@ -33,8 +33,8 @@ ctttctttctttctttctttctttctttctttctttctttctttcttttctttccttctt ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt ctttctttctttctttcttctttctttctttttctttcttttttttttgggatggagtct cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaacctccacct -cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg ->ref_chr20:60702842-60703216 +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagct +>ref_chr20:60702842-60703215 tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac atttgtcattgtctttctttcttttctttctctctctctctttct--------------- @@ -42,4 +42,4 @@ atttgtcattgtctttctttcttttctttctctctctctctttct--------------- cttttc---tttccttctttctttctttctttctttc----------------------- ---------------------------------------tttttttttgggatggagtct cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct -cccaggttcaagcgattgaactcactgcctcagcctcccaagtagctg +cccaggttcaagcgattgaactcactgcctcagcctcccaagtagct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_751763f0a26e66cde66421e24b5f03e2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c09854a1826e6b88567130408713a7f9.msa similarity index 84% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_751763f0a26e66cde66421e24b5f03e2.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_c09854a1826e6b88567130408713a7f9.msa index 2be47406..c0ef88d2 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_751763f0a26e66cde66421e24b5f03e2.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_c09854a1826e6b88567130408713a7f9.msa @@ -1,15 +1,15 @@ ->syndip_1_chr20:24681888-24682378 +>syndip_1_chr20:24681888-24682377 ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg cagcaggaggcaaactgtgaagtacctctctggc-------------------------- ---------------------------------ctggcctttgtgaattaccacagtgc-- ---------------------------------------------------------gggg +------------------------------------------------------------ +------------------------------ctggcctttgtgaattaccacagtgcgggg tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga -ggaggagac ->syndip_2_chr20:24681888-24682378 +ggaggaga +>syndip_2_chr20:24681888-24682377 ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg cagcaggaggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtca @@ -19,8 +19,8 @@ tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga -ggaggagac ->p:HG002_1_chr20:24681888-24682378 +ggaggaga +>p:HG002_1_chr20:24681888-24682377 ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg cagcaggaggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtca @@ -30,19 +30,19 @@ tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga -ggaggagac ->p:HG002_2_chr20:24681888-24682378 +ggaggaga +>p:HG002_2_chr20:24681888-24682377 ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg cagcaggaggcaaactgtgaagtacctctctggc-------------------------- ---------------------------------ctggcctttgtgaattaccacagtgc-- ---------------------------------------------------------gggg +------------------------------------------------------------ +------------------------------ctggcctttgtgaattaccacagtgcgggg tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctctga -ggaggagac ->ref_chr20:24681888-24682378 +ggaggaga +>ref_chr20:24681888-24682377 ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg cagcaggaggcaaactgtgaagtacctctctggc-------------------------- @@ -52,4 +52,4 @@ tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga -ggaggagac +ggaggaga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8f54b846b732cff5d58c80e0ddff85e7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c3ca784845992e7f185ad2e6a992de0e.msa similarity index 87% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_8f54b846b732cff5d58c80e0ddff85e7.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_c3ca784845992e7f185ad2e6a992de0e.msa index 209611ec..24a437db 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8f54b846b732cff5d58c80e0ddff85e7.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_c3ca784845992e7f185ad2e6a992de0e.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:57948901-57949447 +>syndip_1_chr20:57948901-57949446 gatggatggatggatagtggatagatggatgaatagtggatggataaatggattaatgga tggatgaatggatgatggatggatgaatgagatggatggatt----------------ga tggatggatggatggatggatggatggaagaatggatgatggatggatga---------- @@ -7,9 +7,9 @@ tggatggatggatggatggatggatggaagaatggatgatggatggatga---------- agatggatgaatagtggatggataaatggattaatggatggatgaatggatgatggatgg atgaatgagatggatggattgatggatggatggatggatggaagaatggatgatggatgg atgaatgagatgggtggattgatggatggatggatggatggatggatggatggatggatg -g----------------------------------------------------------- -------------- ->syndip_2_chr20:57948901-57949447 +------------------------------------------------------------ +------------ +>syndip_2_chr20:57948901-57949446 gatggatggatggatagtggatagatggatgaatagtggatggataaatggattaatgga tggatgaatggatgatggatggatgaatgagatggatggattgatggatggatggatgga tggatggatggatggatggatggatggaagaatggatgatggatggatgagatggatgga @@ -19,8 +19,8 @@ agatggatgaatagtgaatggataaatggattaatggatggatggatagtggatagatgg atgaat------agtggatggataaatggattaatggatggatgaatggatgatggatgg atgaatgagatggatggattgatggatggatggatggatggatggatggatggaagaatg gatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatggatg -gatggatggatgg ->p:HG002_1_chr20:57948901-57949447 +gatggatggatg +>p:HG002_1_chr20:57948901-57949446 gatggatggatggatagtggatagatggatgaatagtggatggataaatggattaatgga tggatgaatggatgatggatggatgaatgagatggatggattgatggatggatggatgga tggatggatggatggatggatggatggaagaatggatgatggatggatgagatggatgga @@ -30,8 +30,8 @@ agatggatgaatagtgaatggataaatggattaatggatggatggatagtggatagatgg atgaat------agtggatggataaatggattaatggatggatgaatggatgatggatgg atgaatgagatggatggattgatggatggatggatggatggatggatggatggaagaatg gatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatggatg -gatggatggatgg ->p:HG002_2_chr20:57948901-57949447 +gatggatggatg +>p:HG002_2_chr20:57948901-57949446 gatggatggatggatagtggatagatggatgaatagtggatggataaatggattaatgga tggatgaatggatgatggatggatgaatgagatggatggattgatggatggatggatgga tggatggatggatggatggatggatggaaga----------------------------- @@ -40,9 +40,9 @@ tggatggatggatggatggggggttggatggatggatggatggatggatggatagtggat agatggatgaatagtgaatggataaatggattaatggatggatggatagtggatagatg- -tgatg------gatggatggatggatggatggatggatggaagaatggatgatggatgg atgaatgagatgggtggattgatggatggatggatggatggatggatggatggatggatg -g----------------------------------------------------------- -------------- ->ref_chr20:57948901-57949447 +------------------------------------------------------------ +------------ +>ref_chr20:57948901-57949446 gatggatggatggatagtggatagatggatgaatagtggatggataaatggattaatgga tggatgaatggatgatggatggatgaatgagatggatggattgatggatggatggatgga tggatggatggatggatggatggatggaagaatggatgatggatggatgagatggatgga @@ -52,4 +52,4 @@ agatggatgaatagtgaatggataaatggattaatggatggatggatagtggatagatgg atgaat------agtggatggataaatggattaatggatggatgaatggatgatggatgg atgaatgagatggatggattgatggatggatggatggatggatggatggatggaagaatg gatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatggatg -gatggatggatgg +gatggatggatg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_34fd267f3c76809107dec2452a21e62a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c50e1186af8d764e9f4a7ebc3e6ca294.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_34fd267f3c76809107dec2452a21e62a.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_c50e1186af8d764e9f4a7ebc3e6ca294.msa index b106611d..2b643f53 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_34fd267f3c76809107dec2452a21e62a.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_c50e1186af8d764e9f4a7ebc3e6ca294.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:20320239-20320620 +>syndip_1_chr20:20320239-20320619 ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat atatgtaatatatattatatatatgtaatatatataatatatgtaatatattatatatat @@ -26,8 +26,8 @@ ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa tatatattatatatattatatatgtaatatatattatatatattatatatgtaatatata ttatatatattatatatgtaatatatatatatttaaaaacagaaccattatcttttagag -atacatactgaagtgtctggagacatgcttcaagataacccag ->syndip_2_chr20:20320239-20320620 +atacatactgaagtgtctggagacatgcttcaagataaccca +>syndip_2_chr20:20320239-20320619 ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat atatgtaatatata---------------------------ttatatatatgtaatatat @@ -55,8 +55,8 @@ tatatatatttaaaaacagaaccattatcttttagagatac------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -----atactgaagtgtctggagacatgcttcaagataacccag ->p:HG002_1_chr20:20320239-20320620 +----atactgaagtgtctggagacatgcttcaagataaccca +>p:HG002_1_chr20:20320239-20320619 ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat atatgtaatatata---------------------------ttatatatatgtaatatat @@ -84,8 +84,8 @@ tatatatatttaaaaacagaaccattatcttttagagatac------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -----atactgaagtgtctggagacatgcttcaagataacccag ->p:HG002_2_chr20:20320239-20320620 +----atactgaagtgtctggagacatgcttcaagataaccca +>p:HG002_2_chr20:20320239-20320619 ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag taaagatggtatttcagatatatagatatatatatat--tatatatgtaatatatataat atatgtaatatgta--atatatataatatatgtaatatatattatatatatgtaatatat @@ -113,8 +113,8 @@ ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa tatatattatatatattatatatgtaatatatatgtaatatatattatatatgtaatata taatatatattatatatgtaatatatatatatttaaaaacagaaccattatcttttagag -atacatactgaagtgtctggagacatgcttcaagataacccag ->ref_chr20:20320239-20320620 +atacatactgaagtgtctggagacatgcttcaagataaccca +>ref_chr20:20320239-20320619 ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat atatgtaatatata---------------------------ttatatatatgtaatatat @@ -142,4 +142,4 @@ tatatatatttaaaaacagaaccattatcttttagagatac------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -----atactgaagtgtctggagacatgcttcaagataacccag +----atactgaagtgtctggagacatgcttcaagataaccca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_26bf1dadf04f074d20f37e2e9c8a8e4f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c84764c85e3bc2208c93471f25974884.msa similarity index 99% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_26bf1dadf04f074d20f37e2e9c8a8e4f.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_c84764c85e3bc2208c93471f25974884.msa index ce45ee3c..9df36af2 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_26bf1dadf04f074d20f37e2e9c8a8e4f.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_c84764c85e3bc2208c93471f25974884.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63693349-63693833 +>syndip_1_chr20:63693349-63693832 ggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgg gagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccaccttcacca ccaccacctccaccaccacctccaccacctccacctccaccacctccaccacctccacca @@ -125,8 +125,8 @@ ccaccaccacctccaccaccacctccaccaccaccaccacctccaccaccaccacctcca ccaccacctccaccaccaccacctccaccaccacctccaccaccacctccacctccacca ccaccacctgcaccaccacctccacctccaccaccaccaccacctccacctccaccagca gcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgtccctgccata -gc ->syndip_2_chr20:63693349-63693833 +g +>syndip_2_chr20:63693349-63693832 ggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgg gagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccac---cacct ccacctcca---ccacctccacctccacctccaccaccacctccacctccacctccacct @@ -253,8 +253,8 @@ ccacctccacctccaccacctccacca---------------ccaccaccaccaccacct ccaccttcaccaccaccaccacctccaccacctccaccaccacctccaccaccacctcca ccaccacctcctccacctccaccacctccaccaccaccaccacctccacctccaccagca gcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgtccctgccata -gc ->p:HG002_1_chr20:63693349-63693833 +g +>p:HG002_1_chr20:63693349-63693832 ggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgg gagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacctccacct ccacctccacctccaccaccacctccacctccaccaccacctcctccaccaccaccacct @@ -381,8 +381,8 @@ ccacctccacctccaccaccacctcca---------------ccaccaccacctccacct ccaccaccacctccaccaccaccaccaccaccaccaccaccaccaccaccacctccacca ccaccacctgcaccaccacctccacctccaccaccaccaccacctccacctccaccagca gcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgtccctgccata -gc ->p:HG002_2_chr20:63693349-63693833 +g +>p:HG002_2_chr20:63693349-63693832 ggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgg gagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacctccacct ccacctccacctccaccaccacctccacctccaccaccacctcctccaccaccaccacct @@ -509,8 +509,8 @@ ccaccaccacctccaccaccacctccaccaccaccaccacctccaccaccacctccacct ccaccaccacctccaccaccaccaccaccaccaccaccaccaccaccaccacctccacca ccaccacctgcaccaccacctccacctccaccaccaccaccacctccacctccaccagca gcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgtccctgccata -gc ->ref_chr20:63693349-63693833 +g +>ref_chr20:63693349-63693832 ggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgg gagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacctccacct ccacctccacctccaccaccacctccacctccaccaccacctcctccaccacc------- @@ -637,4 +637,4 @@ ccaccacctcca------------------------------------------------ ---------------ccaccaccaccaccaccaccaccaccaccaccaccacctccacca ccaccacctgcaccaccacctccacctccaccaccaccaccacctccacctccaccagca gcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgtccctgccata -gc +g diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_95ddd1fba647caa20dd06cdf75db78e8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c8767647c15df9e79d6194de26f7cdc5.msa similarity index 52% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_95ddd1fba647caa20dd06cdf75db78e8.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_c8767647c15df9e79d6194de26f7cdc5.msa index 1f228f20..9635edad 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_95ddd1fba647caa20dd06cdf75db78e8.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_c8767647c15df9e79d6194de26f7cdc5.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:20354470-20358424 +>syndip_1_chr20:20354470-20358423 tccagtctgggtgacagagagagaccttgtctcaaaaaaaaaaaaaaaaaaatcaggtac agaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcata agggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgagg @@ -40,60 +40,61 @@ tcacactgtgaagggtggtagtcacactgagaggaggtgttcacactgaggggaagtggt cacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtc atagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtca cagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtc -acactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtca -tagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcaca-- -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactgtg -aggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactga -ggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgtgag -gggaggtggtcatactgtgagtgaggaggtagtcacac--tgaggggagggggtcatact +acactgaggggaggtggtcacagtgtgaggggaggtggtcacac---------------- +------------------------tgaggggaggtggtcatagtgtgaggggaggtggtc +acactggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca +ctgaggggaagtggtcacactgaggggaggtggtcaca--ctgaggggaggtggtcatag +tgtgaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca +ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg +tgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcacactgt +gaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgag +gggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcatactgtga +gtgaggaggtagtcacac--tgaggggagggggtcatactgcgagtggaggtagtcacac +tgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacact +gaggggaggtggtcatactg---------------------------------------- +tgaggggaagtggtcacactgaggggaggtggtcatagtgtga--ggggaggtggtcaca +ctgaggggaggtggtcacagtgtgaggggaggtggtcacac--tgaggggaggtggtcac +actgaggggaggtggtcacagtgtgagaggaggtggtcacactgaggggaggtggtcaca +gtgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac +actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca +ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag +tgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca +ctgaggggaggtggtcaca-------------------gtgtgaggggaggtggtcacac +tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaggtggtcatactgt +gagtgaggaggtagtcacactgaggggaagtggtcacactgaggggaggtg--------- +---------------------------------gtcacactgaggggagggggtcatact gcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcacac -tgaggggaagtggtcacactgaggggaggtggtcatactg-------------------- ---------------------tgaggggaagtggtcacactgaggggaggtggtcatagtg -tga--ggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca -c--tgaggggaggtggtcacactgaggggaggtggtcacagtgtgagaggaggtggtcac -actgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca -ctgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcacag -tgtgaggggaggtggtcacactgaggggaggtggtcaca-------------------gt -gtgaggggaggtggtcacactgaggggaggtggtcacactgagaggaggtggtcacactg -aggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacact -gaggggaggtg------------------------------------------gtcacac -tgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcaca -ctgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatactg -tgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggag----------- ------------------------------------------------------------- -------------------------------gtggtcacactgaggggaggtggtcacact -gaggggaggtggtcacagtgtga--ggggaggtggtcacactgaggggaggtggtcacag -tgtacggggaggtggtcatac--tgaggggaggtggtcacagtgtgaggggaggtggtca -cactgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcata -gtgtgaggggaggtggtcacactgaggggaggtggtcaca-c-tgaggagaggtggtcat --------------------agtgtgaggggaggtggtcacac------------------ ------------------------------------------------------------- ------------------------tgaggggaggtggtcacactgaggggaggtggtcata -gtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcac -actgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcaca -gtg--------------------------------------tgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcacat -tgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtg -tgcggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgt -gaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactga -ggggaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtg -tgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcacac -tgagaggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacactga -ggggaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgagg -ggaatggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatga -gaggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatatttg -cctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga ->syndip_2_chr20:20354470-20358424 +tgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacact +gaggggaggtggtcatagtgtgaggggag------------------------------- +------------------------------------------------------------ +----------gtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg +tga--ggggaggtggtcacactgaggggaggtggtcacagtgtacggggaggtggtcata +c--tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcac +actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca +ctgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcac +actgaggggaggtggtcaca-c-tgaggagaggtggtcat-------------------a +gtgtgaggggaggtggtcacac-------------------------------------- +------------------------------------------------------------ +---tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac +actgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca +ctgaggggaggtggtcatagtgtgaggggaggtggtcacagtg----------------- +---------------------tgaggggaggtggtcacactgaggggaggtggtcatagt +gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg +tgaggggaggtggtcacactgtgaggggaggtggtcacattgaggagaggtggtcatagt +gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg +tgaggggaggtggtcacactgaggagaggtggtcatagtgtgcggggaggtggtcacact +gaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacagtg +tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact +gaggggaggtggtcacactgagggaaggtggtcacactgaggggaggtggtcatagtgtg +aggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacact +gaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg +tgaggggaggtgggcacactgtgaggggtggtagtcacactgagaggaggtggtcacact +gaggggaggtggtcacactgaggggaggtggtcacactgaggggaatggtcatactgtga +ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg +ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc +aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag +tggttttacgctatttaacccagtgtcag +>syndip_2_chr20:20354470-20358423 tccagtctgggtgacagagagagaccttgtctc--aaaaaaaaaaaaaaaaatcaggtac agaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcata agggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgagg @@ -134,61 +135,62 @@ atactgtgagtgaggaggtagtcacactgaggggaggggtcatactgcgagtggaggtgg tcacactgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggt cacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtc atagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtca -cagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtc -acactgaggggaggtggtcacagtg-------------------tgaggggaggtggtca -tagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcac -actgtgaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacact----ggggaggtggtcacactgtgaggggaggtggtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacact-------------------- --ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactga -ggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgag -gggaggtggtcacac------tggggaggtggtcacactgtgaggggaggtggtcacact -gtgaggggaggtggtcacac--tgagaggaggtggtcacactgaggggaagtggtcacac +cagtgtgaggggagg----------------------------------------tggtc +acactgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtca +cagtg-------------------tgaggggaggtggtcatagtgtgaggggaggtggtc +acactggggaggtggtcacactgtgaggggaggtggtcacactgtgaggaggtggtcaca +ctgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac +t----ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca +ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg +tgaggggaggtggtcacact---------------------ggggaggtggtcacactgt +gaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgag +gggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac----- +-tggggaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacac +--tgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacact +gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacac tgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcaca +ctgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcac +actgagaggaggtggtcaca--ctgaggggaagtggtcacactgaggggaggtggtcata +ctgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac +actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca +ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag +tgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca +ctgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac +tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaggtggtcatactgt 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-cactgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcac -actgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcata -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcat -actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca -gtgtgcggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcat -actgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcaca -ctgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcac -actgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcaca -ctgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtgacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcacat -tgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtg -tgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgt -gaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactga -ggggaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtg +gtgaggggaggtggtgacactgaggggaggtggtcacactgaggggaggtggtcatagtg +tgaggggaggtggtcacactgtgaggggaggtggtcacattgaggagaggtggtcatagt +gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg tgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcacac -tgagaggaggtggtcacactgaggggaggtggtcacactgaggggaagtggtcacactga -ggggaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgagg -ggaatggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatga -gaggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatatttg -cctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga ->p:HG002_1_chr20:20354470-20358424 +gaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacagtg +tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact +gaggggaggtggtcacactgagggaaggtggtcacactgaggggaggtggtcatagtgtg +aggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacact +gaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg +tgaggggaggtgggcacactgtgaggggtggtagtcacactgagaggaggtggtcacact +gaggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtga +ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg +ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc +aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag +tggttttacgctatttaacccagtgtcag +>p:HG002_1_chr20:20354470-20358423 tccagtctgggtgacagagagagaccttgtctc--aaaaaaaaaaaaaaaaatcaggtac agaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcata agggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgagg @@ -229,61 +231,62 @@ atactgtgagtgaggaggtagtcacactgaggggaggggtcatactgcgagtggaggtgg tcacactgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggt cacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtc atagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtca -cagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtc -acactgaggggaggtggtcacagtg-------------------tgaggggaggtggtca -tagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcac -actgtgaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacact----ggggaggtggtcacactgtgaggggaggtggtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacact-------------------- --ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactga -ggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgag -gggaggtggtcacac------tggggaggtggtcacactgtgaggggaggtggtcacact -gtgaggggaggtggtcacac--tgagaggaggtggtcacactgaggggaagtggtcacac +cagtgtgaggggagg----------------------------------------tggtc +acactgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtca +cagtg-------------------tgaggggaggtggtcatagtgtgaggggaggtggtc +acactggggaggtggtcacactgtgaggggaggtggtcacactgtgaggaggtggtcaca +ctgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac +t----ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca 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+gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcac +actgaggggaggtggtcatagtgtgaggggaggtggtcatactgaggggaggtggtcaca +ctgtgaggggaggtggtcacactgaggagaggtggtcacactgtgaggggaggtggtcac +actgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca +ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatag tgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgagaggaggtggtcacactg -aggggaggtggtcatactgtgagtgaggaagtagtcacactgaggggaagtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacac -tgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcaca -ctgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatactg -tgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact -gtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaggtggtcatactg -tgagtgaggaggtagtcacactgaggggaagtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatac -tgcgagtggaggtagtcacactgtgaagggtggtagtcaca--ctgagaggaggtggtca -cactgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcac -actgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcata -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcat -actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca -gtgtgcggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcat -actgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcaca -ctgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcac -actgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcaca -ctgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtgacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcacat -tgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtg -tgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgt -gaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactga -ggggaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtg +gtgaggggaggtggtgacactgaggggaggtggtcacactgaggggaggtggtcatagtg +tgaggggaggtggtcacactgtgaggggaggtggtcacattgaggagaggtggtcatagt +gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg tgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcacac -tgagaggaggtggtcacactgaggggaggtggtcacactgaggggaagtggtcacactga -ggggaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgagg -ggaatggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatga -gaggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatatttg -cctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga ->p:HG002_2_chr20:20354470-20358424 +gaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacagtg +tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact +gaggggaggtggtcacactgagggaaggtggtcacactgaggggaggtggtcatagtgtg +aggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacact +gaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg +tgaggggaggtgggcacactgtgaggggtggtagtcacactgagaggaggtggtcacact +gaggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtga +ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg +ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc +aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag +tggttttacgctatttaacccagtgtcag +>p:HG002_2_chr20:20354470-20358423 tccagtctgggtgacagagagagaccttgtctcaaaaaaaaaaaaaaaaaaatcaggtac agaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcata agggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgagg @@ -325,61 +328,62 @@ tcacactgtgaagggtggtagtcacactgagaggaggtgttcacactgaggggaagtggt cacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtc atagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtca cagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtc -acactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtca -tagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcaca-- -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactgtg -aggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactga -ggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgtgag -gggaggtggtcatactgtgagtgaggaggtagtcacac--tgaggggagggggtcatact +acactgaggggaggtggtcacagtgtgaggggaggtggtcacac---------------- +------------------------tgaggggaggtggtcatagtgtgaggggaggtggtc +acactggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca +ctgaggggaagtggtcacactgaggggaggtggtcaca--ctgaggggaggtggtcatag +tgtgaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca +ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg +tgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcacactgt +gaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgag +gggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcatactgtga +gtgaggaggtagtcacac--tgaggggagggggtcatactgcgagtggaggtagtcacac +tgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacact +gaggggaggtggtcatactg---------------------------------------- +tgaggggaagtggtcacactgaggggaggtggtcatagtgtga--ggggaggtggtcaca +ctgaggggaggtggtcacagtgtgaggggaggtggtcacac--tgaggggaggtggtcac +actgaggggaggtggtcacagtgtgagaggaggtggtcacactgaggggaggtggtcaca +gtgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac +actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca +ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag +tgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca +ctgaggggaggtggtcaca-------------------gtgtgaggggaggtggtcacac +tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaggtggtcatactgt +gagtgaggaggtagtcacactgaggggaagtggtcacactgaggggaggtg--------- +---------------------------------gtcacactgaggggagggggtcatact gcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcacac -tgaggggaagtggtcacactgaggggaggtggtcatactg-------------------- ---------------------tgaggggaagtggtcacactgaggggaggtggtcatagtg -tga--ggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca -c--tgaggggaggtggtcacactgaggggaggtggtcacagtgtgagaggaggtggtcac -actgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca -ctgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcacag -tgtgaggggaggtggtcacactgaggggaggtggtcaca-------------------gt -gtgaggggaggtggtcacactgaggggaggtggtcacactgagaggaggtggtcacactg -aggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacact -gaggggaggtg------------------------------------------gtcacac -tgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcaca -ctgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatactg -tgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggag----------- ------------------------------------------------------------- -------------------------------gtggtcacactgaggggaggtggtcacact -gaggggaggtggtcacagtgtga--ggggaggtggtcacactgaggggaggtggtcacag -tgtacggggaggtggtcatac--tgaggggaggtggtcacagtgtgaggggaggtggtca -cactgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcata -gtgtgaggggaggtggtcacactgaggggaggtggtcaca-c-tgaggagaggtggtcat --------------------agtgtgaggggaggtggtcacac------------------ ------------------------------------------------------------- ------------------------tgaggggaggtggtcacactgaggggaggtggtcata -gtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcac -actgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcaca -gtg--------------------------------------tgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcacat -tgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtg -tgcggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgt -gaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactga -ggggaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtg -tgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcacac -tgagaggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacactga -ggggaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgagg -ggaatggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatga -gaggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatatttg -cctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga ->ref_chr20:20354470-20358424 -tccagtctgggtgacagagagagaccttgtctc-aaaaaaaaaaaaaaaaaatcaggtac +tgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacact +gaggggaggtggtcatagtgtgaggggag------------------------------- +------------------------------------------------------------ +----------gtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg +tga--ggggaggtggtcacactgaggggaggtggtcacagtgtacggggaggtggtcata +c--tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcac +actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca +ctgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcac +actgaggggaggtggtcaca-c-tgaggagaggtggtcat-------------------a +gtgtgaggggaggtggtcacac-------------------------------------- +------------------------------------------------------------ +---tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac +actgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca +ctgaggggaggtggtcatagtgtgaggggaggtggtcacagtg----------------- +---------------------tgaggggaggtggtcacactgaggggaggtggtcatagt +gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg +tgaggggaggtggtcacactgtgaggggaggtggtcacattgaggagaggtggtcatagt +gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg +tgaggggaggtggtcacactgaggagaggtggtcatagtgtgcggggaggtggtcacact +gaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacagtg +tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact +gaggggaggtggtcacactgagggaaggtggtcacactgaggggaggtggtcatagtgtg +aggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacact +gaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg +tgaggggaggtgggcacactgtgaggggtggtagtcacactgagaggaggtggtcacact +gaggggaggtggtcacactgaggggaggtggtcacactgaggggaatggtcatactgtga +ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg +ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc +aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag +tggttttacgctatttaacccagtgtcag +>ref_chr20:20354470-20358423 +tccagtctgggtgacagagagagaccttgtctca-aaaaaaaaaaaaaaaaatcaggtac agaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcata agggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatagtcacactgagg gaaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcacac @@ -419,40 +423,40 @@ atactgtgagtgaggagctagtcacactgaggggaggggtcatactgcgagtggaggtag tcacactgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggt cacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtc atagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtca -cagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtc -acactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtca -tagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacact----ggggaggtggtcacactgtgaggggaggtggtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacact-------------------- --ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactga -ggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgag -gggaggtggtcacac------tggggaggtggtcacactgtgaggggaggtggtcacact -gtgaggggaggtggtcacac--tgagaggaggtggtcacactgaggggaagtggtcacac -tgagaggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcaca -ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactg -tgagtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcaca -ctgtgaagggtggtagtcacactgagaggaggtggtcaca--ctgaggggaagtggtcac -actgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcata -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcaca---------------------------------------- +cagtgtgaggggagg----------------------------------------tggtc +acactgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtca +cagtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtc +acactggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca +ctgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac +t----ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca +ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg +tgaggggaggtggtcacact---------------------ggggaggtggtcacactgt +gaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgag +gggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac----- +-tggggaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacac +--tgagaggaggtggtcacactgaggggaagtggtcacactgagaggaggtggtcacact +gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacac +tgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcaca +ctgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcac +actgagaggaggtggtcaca--ctgaggggaagtggtcacactgaggggaggtggtcata +ctgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac +actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca ------------------------------------------------------------ -----------------------------------------------------------gt -gtgcggggaggtggtcatactgaggggaggtggtcacactgaggggaggtggtcacactg -aggggaggtggtcatactgtgagt------------------------------------ ------------------------------------------------------------ +--------------------------------------gtgtgcggggaggtggtcatac +tgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgt +gagt-------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------------------------gaggaggtagtcacactgaggggagggggtcatac -tgcgagtggaggtagtcacactgtgaagggtggtagtcaca--ctgagaggaggtggtca -cactgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcac -actgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcat ------------------------------------------------------------ +-----gaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcaca +ctgtgaagggtggtagtcaca--ctgagaggaggtggtcacactgaggggaagtggtcac +actgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcata +gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac +actgaggggaggtggtcacagtgtgcggggaggtggtcat-------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -462,14 +466,15 @@ gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcat ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------actgaggggaggtggtcacagtgt -gaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactga -ggggaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtg -tgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcacac -tgagaggaggtggtcacactgaggggaggtggtcacactgaggggaagtggtcacactga -ggggaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgagg -ggaatggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatga -gaggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatatttg -cctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga +------------------------------------------------------------ +----------------actgaggggaggtggtcacagtgtgaggggaggtggtcacagtg +tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact +gaggggaggtggtcacactgagggaaggtggtcacactgaggggaggtggtcatagtgtg +aggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacact +gaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg +tgaggggaggtgggcacactgtgaggggtggtagtcacactgagaggaggtggtcacact +gaggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtga +ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg +ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc +aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag +tggttttacgctatttaacccagtgtcag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_11e116fedba8bcf09b5d2c98cbaa4d60.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ce6ba4dc0f8a352c89d3dfc839c96d2e.msa similarity index 99% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_11e116fedba8bcf09b5d2c98cbaa4d60.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_ce6ba4dc0f8a352c89d3dfc839c96d2e.msa index d5dd141a..7df1d60e 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_11e116fedba8bcf09b5d2c98cbaa4d60.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_ce6ba4dc0f8a352c89d3dfc839c96d2e.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:64173338-64176431 +>syndip_1_chr20:64173338-64176430 gatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtaga gatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgtccatttccc ctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctg @@ -64,8 +64,8 @@ tctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgt gtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggc ->syndip_2_chr20:64173338-64176431 +gg +>syndip_2_chr20:64173338-64176430 gatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtaga gatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgtccatttccc ctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctg @@ -131,8 +131,8 @@ tcctgtagcatctttccctgtagttgtgtccattccccctccctgg-------------- ------------------------------------------------------------ ----------------------ctcctcctgcagcatctttccctgtagttgtgtccatt tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggc ->p:HG002_1_chr20:64173338-64176431 +gg +>p:HG002_1_chr20:64173338-64176430 gatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtaga gatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgtccatttccc ctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctg @@ -198,8 +198,8 @@ tcctgtagcatctttccctgtagttgtgtccattccccctccctgg-------------- ------------------------------------------------------------ ----------------------ctcctcctgcagcatctttccctgtagttgtgtccatt tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggc ->p:HG002_2_chr20:64173338-64176431 +gg +>p:HG002_2_chr20:64173338-64176430 gatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtaga gatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgtccatttccc ctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctg @@ -265,8 +265,8 @@ tctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgt gtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggc ->ref_chr20:64173338-64176431 +gg +>ref_chr20:64173338-64176430 gatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtaga gatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgtccatttccc ctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctg @@ -332,4 +332,4 @@ tcctgtagcatctttccctgtagttgtgtccattccccctccctggcgtctc-------- tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgt gtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggc +gg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_64dff7b5bf598bbdb48ee4b45e644ad7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_cea716cb5fb96bc6d8bf0051a8d70890.msa similarity index 94% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_64dff7b5bf598bbdb48ee4b45e644ad7.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_cea716cb5fb96bc6d8bf0051a8d70890.msa index a82c95f9..af4d665d 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_64dff7b5bf598bbdb48ee4b45e644ad7.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_cea716cb5fb96bc6d8bf0051a8d70890.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63027966-63029131 +>syndip_1_chr20:63027966-63029130 ctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacg cgggcggggagtggaccggtggggagagggccggtggggagagggccggtggggagagga ccggtggggagggggccggtggagagggggccggtggggagggggccggtggggagagga @@ -35,8 +35,8 @@ tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg cctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg cgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc cgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg ->syndip_2_chr20:63027966-63029131 +tccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc +>syndip_2_chr20:63027966-63029130 ctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacg cgggcggggagtggaccggtggggagagggccggtggggagaggaccggtggggag-ggg ccggtggagagggggccggtggggagggggccggcggggag------------------- @@ -60,7 +60,6 @@ ctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgc aggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatg atgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgg gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc -g----------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -73,8 +72,9 @@ g----------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------------------------------- ->p:HG002_1_chr20:63027966-63029131 +------------------------------------------------------------ +--------------------------------------------------------- +>p:HG002_1_chr20:63027966-63029130 ctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacg cgggcggggagtggaccggtggggagagggccggtggggagaggaccggtggggag-ggg ccggtggagagggggccggtggggagggggccggcggggag------------------- @@ -98,7 +98,6 @@ ctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgc aggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatg atgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgg gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc -g----------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -111,8 +110,9 @@ g----------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------------------------------- ->p:HG002_2_chr20:63027966-63029131 +------------------------------------------------------------ +--------------------------------------------------------- +>p:HG002_2_chr20:63027966-63029130 ctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacg cgggcggggagtggaccggtggggagagggccggtggggagaggaccggtggggag-ggg ccggtggagagggggccggtggggagggggccggtggggagggggccggtggggagagga @@ -149,8 +149,8 @@ tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg cctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg cgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctc cgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg ->ref_chr20:63027966-63029131 +tccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc +>ref_chr20:63027966-63029130 ctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacg cgggcggggagtggaccggtggggagagggccggtggggagaggaccggtggggag-ggg ccggtggagagggggccggtggggagggggccggcggggag------------------- @@ -176,7 +176,7 @@ atgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgg gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtccccc gggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccc ccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtc -ccccg------------------------------------------------------- +cccc-------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -187,4 +187,4 @@ ccccg------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------------------------------- +--------------------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_751f12a6ae4022208996c7a282d999de.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_cf9425969f7f5ed38f54639e08586a04.msa similarity index 87% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_751f12a6ae4022208996c7a282d999de.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_cf9425969f7f5ed38f54639e08586a04.msa index 0403e378..db141b39 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_751f12a6ae4022208996c7a282d999de.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_cf9425969f7f5ed38f54639e08586a04.msa @@ -1,40 +1,40 @@ ->syndip_1_chr20:57190156-57190529 +>syndip_1_chr20:57190156-57190528 gctggagagagtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaacc agagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggcc----agagt gagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgag gctggagagagtgagccaggaaccagaggaggtgaggccaga----gtgagtgaggagct tgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggctggagagcgt gagtgaggagcccgagggggtgaggctggagagagtgagtgaggagcccaagggggtgaa -gccgaggtgggtatgggg ->syndip_2_chr20:57190156-57190529 +gccgaggtgggtatggg +>syndip_2_chr20:57190156-57190528 gctggagagagtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaacc agagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagt gagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgag gctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtgagtgaggagcc cgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctggagagagt gagtgaggagcccaagggggtgaagccgaggtgggt------------------------ -------------atgggg ->p:HG002_1_chr20:57190156-57190529 +------------atggg +>p:HG002_1_chr20:57190156-57190528 gctggagagagtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaacc agagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagt gagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgag gctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtgagtgaggagcc cgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctggagagagt gagtgaggagcccaagggggtgaagccgaggtgggt------------------------ -------------atgggg ->p:HG002_2_chr20:57190156-57190529 +------------atggg +>p:HG002_2_chr20:57190156-57190528 gctggagagagtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaacc agagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagt gagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgag gctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtgagtgaggagcc cgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctggagagcgt gagtgaggagcccgagggggtgaggctggagagagtgagtgaggagcccaagggggtgaa -gccgaggtgggtatgggg ->ref_chr20:57190156-57190529 +gccgaggtgggtatggg +>ref_chr20:57190156-57190528 gctggagagagtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaacc agagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagt gagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgag gctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtgagtgaggagcc cgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctggagagcgt gagtgaggagcccgagggggtgaggctggagagagtgagtgaggagcccaagggggtgaa -gccgaggtgggtatgggg +gccgaggtgggtatggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_71fa13a9fc89d5f2aef29ccb10589a60.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d2242ccd448a7c982cfcff72641d3495.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_71fa13a9fc89d5f2aef29ccb10589a60.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_d2242ccd448a7c982cfcff72641d3495.msa index cf2b055d..78229f17 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_71fa13a9fc89d5f2aef29ccb10589a60.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_d2242ccd448a7c982cfcff72641d3495.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:51952383-51954993 +>syndip_1_chr20:51952383-51954992 ctctgtctcaaaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattat ttagttttatagcattacattcaagtttttatagcattacaattcctagattctattttc aaatattgatttgcttaa--ttttttttttttttgagatggggttttgctctgtcgccca @@ -47,8 +47,8 @@ ccacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggc ttgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagat tacaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggt tgtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtc -ctgcattttcatcaggtaaagaaagcttttcatgtttcactgag ->syndip_2_chr20:51952383-51954993 +ctgcattttcatcaggtaaagaaagcttttcatgtttcactga +>syndip_2_chr20:51952383-51954992 ctctgtctc-aaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattat ttagttttatagcattacattcaagtttttatagcattacaattcctagattctattttc aaatattgatttgcttaa-tttttttttttttttgagatggggttttgctctgtcgccca @@ -97,8 +97,8 @@ ccacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggc ttgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagat tacaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggt tgtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtc -ctgcattttcatcaggtaaagaaagcttttcatgtttcactgag ->p:HG002_1_chr20:51952383-51954993 +ctgcattttcatcaggtaaagaaagcttttcatgtttcactga +>p:HG002_1_chr20:51952383-51954992 ctctgtctc-aaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattat ttagttttatagcattacattcaagtttttatagcattacaattcctagattctattttc aaatattgatttgcttaa-tttttttttttttttgagatggggttttgctctgtcgccca @@ -147,8 +147,8 @@ ccacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggc ttgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagat tacaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggt tgtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtc -ctgcattttcatcaggtaaagaaagcttttcatgtttcactgag ->p:HG002_2_chr20:51952383-51954993 +ctgcattttcatcaggtaaagaaagcttttcatgtttcactga +>p:HG002_2_chr20:51952383-51954992 ctctgtctcaaaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattat ttagttttatagcattacattcaagtttttatagcattacaattcctagattctattttc aaatattgatttgcttaa--ttttttttttttttgagatggggttttgctctgtcgccca @@ -197,8 +197,8 @@ ccacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggc ttgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagat tacaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggt tgtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtc -ctgcattttcatcaggtaaagaaagcttttcatgtttcactgag ->ref_chr20:51952383-51954993 +ctgcattttcatcaggtaaagaaagcttttcatgtttcactga +>ref_chr20:51952383-51954992 ctctgtctc-aaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattat ttagttttatagcattacattcaagtttttatagcattacaattcctagattctattttc aaatattgatttgcttaattttttttttttttttgagatggggttttgctctgtcgccca @@ -247,4 +247,4 @@ ccacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggc ttgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagat tacaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggt tgtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtc -ctgcattttcatcaggtaaagaaagcttttcatgtttcactgag +ctgcattttcatcaggtaaagaaagcttttcatgtttcactga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3e3662b58e37c8d091efddc27cbaa4e4.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d4b126e5900cc00f6c75e82b4be27559.msa similarity index 90% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_3e3662b58e37c8d091efddc27cbaa4e4.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_d4b126e5900cc00f6c75e82b4be27559.msa index 86814ea1..7f48c7be 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3e3662b58e37c8d091efddc27cbaa4e4.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_d4b126e5900cc00f6c75e82b4be27559.msa @@ -1,40 +1,40 @@ ->syndip_1_chr20:34235798-34236082 +>syndip_1_chr20:34235798-34236081 aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaagg aaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaggaagcgggagggaggg aagaaggaaggaaggaggagggagggaagaatgaaggaaggaaggaaggaaggaaggaag gaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaa ggaaggaggagggagggagggaagcaggaaagaaggaaggaaggagaaagagagaaagag agagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagag -aaagag ->syndip_2_chr20:34235798-34236082 +aaaga +>syndip_2_chr20:34235798-34236081 aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaagg aaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaggaagcgggagggaggg aagaaggaaggaaggaggagggagggaagaatgaaggaaggaaggaaggaaggaaggaag gaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaa ggaaggaggagggagggagggaagcaggaaagaaggaaggaaggagaaagagagaaagag agagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagag -aaagag ->p:HG002_1_chr20:34235798-34236082 +aaaga +>p:HG002_1_chr20:34235798-34236081 aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaagg aaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaaggaa-ggaaggaagga aggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggaaggaag gaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaa ggaaggaggagggagggagggaagaaggaaagaaggaaggaaggagaaagagagaaagag agagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagag -aaagag ->p:HG002_2_chr20:34235798-34236082 +aaaga +>p:HG002_2_chr20:34235798-34236081 aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaagg aaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaaggaa-ggaaggaagga aggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggaaggaag gaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaa ggaaggaggagggagggagggaagaaggaaagaaggaaggaaggagaaagagagaaagag agagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagag -aaagag ->ref_chr20:34235798-34236082 +aaaga +>ref_chr20:34235798-34236081 aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaagg aaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaaggaa------------ -------------------------------------------ggaaggaaggaaggaag gaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagggagggaaga- -------------------------aggaaagaaggaaggaaggagaaagagagaaagag agagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagag -aaagag +aaaga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_cd64f44baadcf644191d9a4521bc7d85.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d68e9f67e20c4afd7f0f9e6fada0a063.msa similarity index 91% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_cd64f44baadcf644191d9a4521bc7d85.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_d68e9f67e20c4afd7f0f9e6fada0a063.msa index 189cda58..60e6926f 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_cd64f44baadcf644191d9a4521bc7d85.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_d68e9f67e20c4afd7f0f9e6fada0a063.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:55944172-55945276 +>syndip_1_chr20:55944172-55945275 atggcaccactgcattccagctgggcaacagagagagactctttcttaaatatatatatt ttatatatatatagatacacacacacacacacacacacacac------------------ ----------------atatatatatatatatatatatatatatatatatgcatgcatgc @@ -19,8 +19,8 @@ gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagat agtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctat -ctagatagtatctgtcgctatctagatatctatctagatagta ->syndip_2_chr20:55944172-55945276 +ctagatagtatctgtcgctatctagatatctatctagatagt +>syndip_2_chr20:55944172-55945275 atggcaccactgcattccagctgggcaacagagagagactctttcttaaatatatatatt ttatatatatatagatacacacacacacacacacacacacacacacacacacacacacac acatatatatatatatatatatatatatatatatatatatatatatatatgcatgcatgc @@ -38,11 +38,11 @@ tagatagtatctatctagatatcggtctagat-----agtatctatctagatatctgtgt agatgtctagatatctatctagatat---tatctatctagatatctgtcgctatctagat atctatctagatatctgtcgctatctagatatctatctaga---tatctgtcgctatcta gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagta----------------------------------- +tatctagatatctatctagatagt------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------- ->p:HG002_1_chr20:55944172-55945276 +------------------------------------------ +>p:HG002_1_chr20:55944172-55945275 atggcaccactgcattccagctgggcaacagagagagactctttcttaaatatatatatt ttatatatatatagatacacacacacacacacacacacacacacacacacacacacacac acatatatatatatatatatatatatatatatatatatatatatatatatgcatgcatgc @@ -60,11 +60,11 @@ tagatagtatctatctagatatctgtgtagatgtctagatatctatctagatat-----t atctatctagatatctgtcgctatctagatatctatctagatatctgtcgctatctagat atctatctagatatctgtcgctatctagatatctatctaga---tatctgtcgctatcta gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagta----------------------------------- +tatctagatatctatctagatagt------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------- ->p:HG002_2_chr20:55944172-55945276 +------------------------------------------ +>p:HG002_2_chr20:55944172-55945275 atggcaccactgcattccagctgggcaacagagagagactctttcttaaatatatatatt ttatatatatatagatacacacacacacacacacacacacac------------------ ----------------atatatatatatatatatatatatatatatatatgcatgcatgc @@ -85,8 +85,8 @@ gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagat agtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctat -ctagatagtatctgtcgctatctagatatctatctagatagta ->ref_chr20:55944172-55945276 +ctagatagtatctgtcgctatctagatatctatctagatagt +>ref_chr20:55944172-55945275 atggcaccactgcattccagctgggcaacagagagagactctttcttaaatatatatatt ttatatatatatagatacacacacacacacacacacacacac------------------ ----------------atatatatatatatatatatatatatatatatatgcatgcatgc @@ -106,5 +106,5 @@ atctatctagatatctgtcgctatctagatatctatctagatagtatctgtcgctatcta gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagat -agta-------------------------------------------------------- -------------------------------------------- +agt--------------------------------------------------------- +------------------------------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_205f920d471a6a80b754572645188116.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d758d8d416dd205a6f2a3a988afe6ca4.msa similarity index 91% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_205f920d471a6a80b754572645188116.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_d758d8d416dd205a6f2a3a988afe6ca4.msa index 38013a4c..e5a411fe 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_205f920d471a6a80b754572645188116.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_d758d8d416dd205a6f2a3a988afe6ca4.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:62830512-62830939 +>syndip_1_chr20:62830512-62830938 cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta cccatgtaccacagtcccccaccccccaccgtgctccacc-------------------- @@ -10,8 +10,8 @@ cccccatgacagtcccccaacccccaccacagtcccccaacccccaccacagtccccacc ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatccccca-c ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt -ggcgcctttggcccctctgaccttcca ->syndip_2_chr20:62830512-62830939 +ggcgcctttggcccctctgaccttcc +>syndip_2_chr20:62830512-62830938 cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta cccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccca @@ -23,8 +23,8 @@ cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt -ggcgcctttggcccctctgaccttcca ->p:HG002_1_chr20:62830512-62830939 +ggcgcctttggcccctctgaccttcc +>p:HG002_1_chr20:62830512-62830938 cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta cccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccca @@ -36,8 +36,8 @@ cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt -ggcgcctttggcccctctgaccttcca ->p:HG002_2_chr20:62830512-62830939 +ggcgcctttggcccctctgaccttcc +>p:HG002_2_chr20:62830512-62830938 cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta cccatgtaccacagtcccccaccccccaccgtgctccacc-------------------- @@ -49,8 +49,8 @@ cccccatgacagtcccccaacccccaccacagtcccccaacccccaccacagtccccacc ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatccccca-c ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt -ggcgcctttggcccctctgaccttcca ->ref_chr20:62830512-62830939 +ggcgcctttggcccctctgaccttcc +>ref_chr20:62830512-62830938 cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta cccatgtaccacagtccccc---------------------------------------- @@ -62,4 +62,4 @@ cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt -ggcgcctttggcccctctgaccttcca +ggcgcctttggcccctctgaccttcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ca43b50e2a5d770bb34202d8a7b62421.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d7c982150b9084cabc20a2d51cc2fab7.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_ca43b50e2a5d770bb34202d8a7b62421.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_d7c982150b9084cabc20a2d51cc2fab7.msa index 79f62fef..58ba55a3 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ca43b50e2a5d770bb34202d8a7b62421.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_d7c982150b9084cabc20a2d51cc2fab7.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:20356430-20357911 +>syndip_1_chr20:20356430-20357910 ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag tgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca ctgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactg @@ -31,8 +31,8 @@ gaggggaggtggtcatactgtga--ggggaagtggtcacactgaggggaggtggtcatag tgtgaggggaggtggtcacac--tgaggggaggtggtcacactgaggggaggtggtcaca gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcat actgaggggaggtggtcacagtgtgaggggaggtggtcaca------------------- ---ctgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac ------------------------------------------------------------a +--ctgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtca- +----------------------------------------------------------ca ctgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcatag tgtgaggggaggtggtcacactgaggggaggtggtcaca--ctgaggagaggtggtcata gtgtgaggggaggtggtcacac--tgaggggaggtggtcacactgaggggaggtggtcat @@ -45,8 +45,8 @@ ttgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagt gtgcggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcac ->syndip_2_chr20:20356430-20357911 +gtgaggggaggtggtca +>syndip_2_chr20:20356430-20357910 ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag tgtgaggggagatggtcacactgaggggaggtggtcacagtg------------------ -tgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactg @@ -79,8 +79,8 @@ gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatac tgcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcaca --ctgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcac actgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcat ------------------------------------------------------------a +gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtca- +----------------------------------------------------------ta ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag tgtgcggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcata --ctgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcac @@ -93,8 +93,8 @@ ttgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagt gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcac ->p:HG002_1_chr20:20356430-20357911 +gtgaggggaggtggtca +>p:HG002_1_chr20:20356430-20357910 ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag tgtgaggggagatggtcacactgaggggaggtggtcacagtg------------------ -tgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactg @@ -127,8 +127,8 @@ gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatac tgcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcaca --ctgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcac actgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcat ------------------------------------------------------------a +gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtca- +----------------------------------------------------------ta ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag tgtgcggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcata --ctgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcac @@ -141,8 +141,8 @@ ttgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagt gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcac ->p:HG002_2_chr20:20356430-20357911 +gtgaggggaggtggtca +>p:HG002_2_chr20:20356430-20357910 ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag tgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca ctgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactg @@ -189,8 +189,8 @@ ttgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagt gtgcggggaggtggtcacactgcggggaggtggtcatactgaggggaggtggtcacagtg tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcac ->ref_chr20:20356430-20357911 +gtgaggggaggtggtca +>ref_chr20:20356430-20357910 ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag tgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca ctgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactg @@ -223,7 +223,7 @@ gaggggaggtggtcatactgtga--ggggaagtggtcacactgaggggaggtggtcatag tg---------------------tgaggggaggtggtcacactgaggggaggtggtcaca gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcat actgaggggaggtggtcacagtgtgaggggaggtggtcaca------------------- -gtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac +gtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtca- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ @@ -237,4 +237,4 @@ gtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------- +----------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d82a691e489dc8fab00bca3d0d072f7e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d82a691e489dc8fab00bca3d0d072f7e.msa deleted file mode 100644 index e85bad4b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d82a691e489dc8fab00bca3d0d072f7e.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:5041841-5042369 -aaccctttttcaagagtctctccccagctgctgctagcgggattttttttttaactctct -atcctatttaacctcctcactgatgaccttttaatgcgtaac------------------ -----------ttttttttttttttttttttttgagacggagtctcgctctcccaggctgg -agtgcagtggtgtgatctcggctcactgcaacctgtgcctcccaggttcaagcgatctcc -tgcctcagcctccccagtacctaggattacaggtgcgcgcctccagcatagctaatgttt -gtatttttagtagagacggggtttcaccatgttggccaggctggttatgcataacttttt -atcacagatgtttgatctcagttttaatcttttcaacatttgtaaacccttggttcattg -tgcttctccctttattactc------------ttttttttttttttttgagacggagttt -cgctcttgttgcccaggctggagtgcagtggcgcactctcggttcactgcaatctccacc -tcataggttcaagcgat------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------ ->syndip_2_chr20:5041841-5042369 -aaccctttttcaagagtctctccccagctgctgctagcgggattttttttttaactctct -atcctatttaacctcctcactgatgaccttttaatgcgtaactttttttttttttttttt -ttttttttttttttttttttttttttttttttgagacggagtctcgctctcccaggctgg -agtgcagtggtgtgatctcggctcactgcaacctgtgcctcccaggttcaagcgatctcc -tgcctcagcctccccagtacctaggattacaggtgcgcgcctccagcatagctaatgttt -gtatttttagtagagacggggtttcaccatgttggccaggctggttatgcataacttttt -atcacagatgtttgatctcagttttaatcttttcaacatttgtaaacccttggttcattg -tgcttctccctttattactcttttttttttttttttttttttttttttgagacggagttt -cgctcttgttgcccaggctggagtgcagtggcgcactctcggttcactgcaatctccacc -tcataggttcaagcgat------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------ ->p:HG002_1_chr20:5041841-5042369 -aaccctttttcaagagtctctccccagctgctgctagcgggattttttttttaactctct -atcctatttaacctcctcactgatgaccttttaatgcgtaactttttttttttttttttt -ttttttttttttttttttttttttttttttttgagacggagtctcgctctcccaggctgg -agtgcagtggtgtgatctcggctcactgcaacctgtgcctcccaggttcaagcgatctcc -tgcctcagcctccccagtacctaggattacaggtgcgcgcctccagcatagctaatgttt -gtatttttagtagagacggggtttcaccatgttggccaggctggttatgcataacttttt -atcacagatgtttgatctcagttttaatcttttcaacatttgtaaacccttggttcattg -tgcttctccctttattactcttttttttttttttttttttttttttttgagacggagttt -cgctcttgttgcccaggctggagtgcagtggcgcactctcggttcactgcaatctccacc -tcataggttcaagcgat------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------ ->p:HG002_2_chr20:5041841-5042369 -aaccctttttcaagagtctctccccagctgctgctagcgggattttttttttaactctct -atcctatttaacctcctcactgatgaccttttaatgcgtaac------------------ -----------ttttttttttttttttttttttgagacggagtctcgctctcccaggctgg -agtgcagtggtgtgatctcggctcactgcaacctgtgcctcccaggttcaagcgatctcc -tgcctcagcctccccagtacctaggattacaggtgcgcgcctccagcatagctaatgttt -gtatttttagtagagacggggtttcaccatgttggccaggctggttatgcataacttttt -atcacagatgtttgatctcagttttaatcttttcaacatttgtaaacccttggttcattg -tgcttctccctttattactc------------ttttttttttttttttgagacggagttt -cgctcttgttgcccaggctggagtgcagtggagcactctcggttcactgcaacctccacc -tcataggttcaagcgattctcctgcctcagcctcctgagtagctgggattacaggtgccc -accaccatgcccttttttttttttgagacggagtttcgctcttgttgcccaggctggagt -gcagtggcgcactctcggttcactgcaatctccacctcataggttcaagcgat ->ref_chr20:5041841-5042369 -aaccctttttcaagagtctctccccagctgctgctagcgggattttttttttaactctct -atcctatttaacctcctcactgatgaccttttaatgcgtaac------------------ -----------ttttttttttttttttttttttgagacggagtctcgctctcccaggctgg -agtgcagtggtgtgatctcggctcactgcaacctgtgcctcccaggttcaagcgatctcc -tgcctcagcctccccagtacctaggattacaggtgcgcgcctccagcatagctaatgttt -gtatttttagtagagacggggtttcaccatgttggccaggctggttatgcataacttttt -atcacagatgtttgatctcagttttaatcttttcaacatttgtaaacccttggttcattg -tgcttctccctttattactcttttttttttttttttttttttttttttgagacggagttt -cgctcttgttgcccaggctggagtgcagtggcgcactctcggttcactgcaatctccacc -tcataggttcaagcgat------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_146844a1e2baa87f3462a854600507de.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d83685774be2675f1a182646478490ed.msa similarity index 85% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_146844a1e2baa87f3462a854600507de.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_d83685774be2675f1a182646478490ed.msa index b7aa8658..73601803 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_146844a1e2baa87f3462a854600507de.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_d83685774be2675f1a182646478490ed.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:21120112-21120640 +>syndip_1_chr20:21120112-21120639 acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta @@ -7,8 +7,8 @@ tgtatatatatatata-------------------------------------------- --------------------tatatttatatatatatatatatt----tatatatatata tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc -atccacattttggagagcagtctactttcctcaaagcctactgcttcaa ->syndip_2_chr20:21120112-21120640 +atccacattttggagagcagtctactttcctcaaagcctactgcttca +>syndip_2_chr20:21120112-21120639 acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta @@ -17,8 +17,8 @@ tgtatatatatatata-------------------------------------------- --------------------tatatttatatatatatatatatttatatatatatatata tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc -atccacattttggagagcagtctactttcctcaaagcctactgcttcaa ->p:HG002_1_chr20:21120112-21120640 +atccacattttggagagcagtctactttcctcaaagcctactgcttca +>p:HG002_1_chr20:21120112-21120639 acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta @@ -27,8 +27,8 @@ tgtatatatatatata-------------------------------------------- --------------------tatatttatatatatatatatatttatatatatatatata tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc -atccacattttggagagcagtctactttcctcaaagcctactgcttcaa ->p:HG002_2_chr20:21120112-21120640 +atccacattttggagagcagtctactttcctcaaagcctactgcttca +>p:HG002_2_chr20:21120112-21120639 acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta @@ -37,8 +37,8 @@ tgtatatatatatata-------------------------------------------- --------------------tatatttatatatatatatatatt----tatatatatata tatttatatatatatatatatatatggagagagagagatttatttttaggaagtggttca tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc -atccacattttggagagcagtctactttcctcaaagcctactgcttcaa ->ref_chr20:21120112-21120640 +atccacattttggagagcagtctactttcctcaaagcctactgcttca +>ref_chr20:21120112-21120639 acagactgagactttgtcttaaaatcaaattaatttaatttaaaaaacaaatgcctttga gcaaagtgctgttagtaacctcatgtcttcctgtattcatcagggttcttcagagaaaca gaaccagtaggacacacacacacgcacacacacacacgtgtgtgtatatatatgtgtgta @@ -47,4 +47,4 @@ tatttatatatatatatatttatatatatatatttatatatatatatttatatatatata tatttatatatatatatatttatatatatatatttatatatatatatatttatatatata tatttatatatatatatatttatatggagagagagagatttatttttaggaagtggttca tgagattgtgagggacttcattcttttctcctaaggccttcaactgactggatgaggccc -atccacattttggagagcagtctactttcctcaaagcctactgcttcaa +atccacattttggagagcagtctactttcctcaaagcctactgcttca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_198bdf87b60e4ea96dbdacfeb79a01dc.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_da9e583f8bb0c9329678fe2798c29f69.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_198bdf87b60e4ea96dbdacfeb79a01dc.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_da9e583f8bb0c9329678fe2798c29f69.msa index d10b6f5d..518d1963 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_198bdf87b60e4ea96dbdacfeb79a01dc.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_da9e583f8bb0c9329678fe2798c29f69.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63028776-63029503 +>syndip_1_chr20:63028776-63029502 caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca aacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg @@ -23,8 +23,7 @@ gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct ccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca -t ->syndip_2_chr20:63028776-63029503 +>syndip_2_chr20:63028776-63029502 caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca aa---------------------------------------------------------- @@ -49,8 +48,7 @@ gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct ccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagtttg ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca -t ->p:HG002_1_chr20:63028776-63029503 +>p:HG002_1_chr20:63028776-63029502 caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca aa---------------------------------------------------------- @@ -75,8 +73,7 @@ gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct ccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagtttg ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca -t ->p:HG002_2_chr20:63028776-63029503 +>p:HG002_2_chr20:63028776-63029502 caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca aacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg @@ -101,8 +98,7 @@ gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct ccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg ccaacgtccatgcacgtctcagcctctcagcctggactggacaactcggcttcgggaatt catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgaattca -t ->ref_chr20:63028776-63029503 +>ref_chr20:63028776-63029502 caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca aa---------------------------------------------------------- @@ -127,4 +123,3 @@ gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct ccgcgtctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca -t diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_37a09937c45cf5969ce12d15082abfbb.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ddb507ec4de0d55fd44561115d512b4c.msa similarity index 87% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_37a09937c45cf5969ce12d15082abfbb.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_ddb507ec4de0d55fd44561115d512b4c.msa index 96858d9d..d1f1f4b4 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_37a09937c45cf5969ce12d15082abfbb.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_ddb507ec4de0d55fd44561115d512b4c.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:49834009-49834659 +>syndip_1_chr20:49834009-49834658 gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta atattagcttgtctctctctctctctctctctctctctctctctctctctctctc----- @@ -9,8 +9,8 @@ acagtgtgtatatatatatatactgtgtgtatatatatatatactgtata---------- ---------------------------------------tgtatatatatatatatactg tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc -aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag ->syndip_2_chr20:49834009-49834659 +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaa +>syndip_2_chr20:49834009-49834658 gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta atattagcttgtctctctctctctctctctctctctctctctctctctctctctctctct @@ -21,8 +21,8 @@ gtgtatatatatatatactgtatatatatatatactgtgtatatatatatactgtatata tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc -aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag ->p:HG002_1_chr20:49834009-49834659 +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaa +>p:HG002_1_chr20:49834009-49834658 gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta atattagcttgtctctctctctctctctctctctctctctctctctctctctctctctct @@ -33,8 +33,8 @@ gtgtatatatatatatactgtatatatatatatactgtgtatatatatatactgtatata tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc -aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag ->p:HG002_2_chr20:49834009-49834659 +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaa +>p:HG002_2_chr20:49834009-49834658 gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta atattagcttgtctctctctctctctctctctctctctctctctctctctctctc----- @@ -45,8 +45,8 @@ acagtgtgtatatatatatatactgtgtgtatatatatatatactgtata---------- ---------------------------------------tgtatatatatatatatactg tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg aaatacattcattttctctgttgggtagattgatttgacctaactttgagcctcaatctc -aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag ->ref_chr20:49834009-49834659 +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaa +>ref_chr20:49834009-49834658 gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta atattagcttg--tctctctctctctctctctctctctctctctctctctctctctctct @@ -57,4 +57,4 @@ gtgtatatatatatatactgtgtatatatatatactgtgtatatatatatactgtatata tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc -aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaag +aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_047c63d2654e7637150b4279117c89de.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ddb6122dabcdfbfdfd1b60aa0d3cffd6.msa similarity index 91% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_047c63d2654e7637150b4279117c89de.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_ddb6122dabcdfbfdfd1b60aa0d3cffd6.msa index 0cb1fc7f..818a0ba0 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_047c63d2654e7637150b4279117c89de.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_ddb6122dabcdfbfdfd1b60aa0d3cffd6.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:62360090-62360813 +>syndip_1_chr20:62360090-62360812 aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca @@ -14,8 +14,8 @@ gtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtgggtgg gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga -gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc ->syndip_2_chr20:62360090-62360813 +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaag +>syndip_2_chr20:62360090-62360812 aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca @@ -31,8 +31,8 @@ ggtg-------------------------------------------------------- gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga -gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc ->p:HG002_1_chr20:62360090-62360813 +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaag +>p:HG002_1_chr20:62360090-62360812 aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca @@ -48,8 +48,8 @@ ggtg-------------------------------------------------------- gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga -gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc ->p:HG002_2_chr20:62360090-62360813 +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaag +>p:HG002_2_chr20:62360090-62360812 aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca @@ -65,8 +65,8 @@ gtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtgggtgg gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga -gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc ->ref_chr20:62360090-62360813 +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaag +>ref_chr20:62360090-62360812 aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca @@ -82,4 +82,4 @@ ggt--------------------------------------------------------- gtgggtagaaggataggtaggtgggtgggtgggtggatgggtgggtggagggatagatgg gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga -gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaagc +gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6f2f5299f80273895addda455b7332af.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_df55c8c1ea86802a42a7e9b21d75a6f1.msa similarity index 88% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_6f2f5299f80273895addda455b7332af.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_df55c8c1ea86802a42a7e9b21d75a6f1.msa index e922cf47..fd3568ef 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6f2f5299f80273895addda455b7332af.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_df55c8c1ea86802a42a7e9b21d75a6f1.msa @@ -1,40 +1,40 @@ ->syndip_1_chr20:23560839-23561199 +>syndip_1_chr20:23560839-23561198 gtattctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttc ttcagcattcctttctctttctttctttctttctttctttctttccttccttccttcctt ccttccttccttccttccttccttccttccttc--------------------------- ------------------------------------------------------------ --------------------------------ctttctttctttctttctttctttcttt ctttctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgt -tgcccaggctgta ->syndip_2_chr20:23560839-23561199 +tgcccaggctgt +>syndip_2_chr20:23560839-23561198 gtattctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttc ttcagcattcctttctctttctttctttctttctttctttctttctttctttctttcttt ccttctttccttccttccttccttccttccttccttccttccttccttccttccttcctt ccttctttccttctttccttctttccttctttccttctttccttctttccttctttcctt ctttctttctttctttccttctttccttctttctttctttctttctttctttctttcttt ctttctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgt -tgcccaggctgta ->p:HG002_1_chr20:23560839-23561199 +tgcccaggctgt +>p:HG002_1_chr20:23560839-23561198 gtattctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttc ttcagcattcctttctctttctttctttctttctttctttctttctttctttctttcttt ccttctttccttccttccttccttccttccttccttccttccttccttccttccttcttt ccttctttccttctttccttctttccttctttccttctttccttctttccttctttcctt ctttctttctttctttctttctttccttctttctttctttctttctttctttctttcttt ctttctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgt -tgcccaggctgta ->p:HG002_2_chr20:23560839-23561199 +tgcccaggctgt +>p:HG002_2_chr20:23560839-23561198 gtattctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttc ttcagcattcctttctctttctttctttctttctttctttctttctttctttctttcttt ccttctttccttccttccttccttccttccttc--------------------------- ------------------------------------------------------------ --------------------------------ctttctttctttctttctttctttcttt ctttctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgt -tgcccaggctgta ->ref_chr20:23560839-23561199 +tgcccaggctgt +>ref_chr20:23560839-23561198 gtattctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttc ttcagcattcctttctctttctttctttctttctttctttctttctttctttctttcttt ccttctttccttccttccttccttccttccttccttccttccttccttccttccttcctt ccttctttccttctttccttctttccttctttccttctttccttctttccttctttcc-- ----------ttctttccttctttccttctttctttctttctttctttctttctttcttt ctttctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgt -tgcccaggctgta +tgcccaggctgt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_73d49ee7e8516143213fa7125202aeab.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e449e9cc3dfd676b949352d747ef2fae.msa similarity index 88% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_73d49ee7e8516143213fa7125202aeab.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_e449e9cc3dfd676b949352d747ef2fae.msa index 54b133c9..48e09ece 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_73d49ee7e8516143213fa7125202aeab.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_e449e9cc3dfd676b949352d747ef2fae.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:37361652-37362159 +>syndip_1_chr20:37361652-37362158 catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg agtgctgctgagggc--------------------------------------------- @@ -7,8 +7,8 @@ tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact -gcagcctcaaactcctgggtgcaagcaa ->syndip_2_chr20:37361652-37362159 +gcagcctcaaactcctgggtgcaagca +>syndip_2_chr20:37361652-37362158 catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg agtgctgctgagggcctctgtgtgcaggtagagatgccggggtctctgtgtgcag----- @@ -17,8 +17,8 @@ tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact -gcagcctcaaactcctgggtgcaagcaa ->p:HG002_1_chr20:37361652-37362159 +gcagcctcaaactcctgggtgcaagca +>p:HG002_1_chr20:37361652-37362158 catcaggggtggggcagctgggcgctctcggaaagatgacctacggctgggagagagcaa aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg agtgctgctgagggcctctgtgtgcaggtagagatgccggggtctctgtgtgcag----- @@ -27,8 +27,8 @@ tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact -gcagcctcaaactcctgggtgcaagcaa ->p:HG002_2_chr20:37361652-37362159 +gcagcctcaaactcctgggtgcaagca +>p:HG002_2_chr20:37361652-37362158 catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg agtgctgctgagggc--------------------------------------------- @@ -37,8 +37,8 @@ tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact -gcagcctcaaactcctgggtgcaagcaa ->ref_chr20:37361652-37362159 +gcagcctcaaactcctgggtgcaagca +>ref_chr20:37361652-37362158 catcaggggtggggcagctgggggctctcggaaagatgacctacggctgggagagagcaa aacttgccacctcagtgttctctgtgatcctctcctgacactgagcaggggcagggcagg agtgctgctgagggcctctgtgtgcaggtagagatgccggggtctctgtgtgcaggtaga @@ -47,4 +47,4 @@ tgtgcaggtagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtg caggtagagatgtagagatgctggggtctctgtgtgcaggtagagatgctggggtctctg tgtgcaggcagagatgctgaagcccaggttagctcttatttatgtctttatttatttttt tgagacaaggtctcactctgttgcccaggctggagtgcagtggtgtaatcatagctcact -gcagcctcaaactcctgggtgcaagcaa +gcagcctcaaactcctgggtgcaagca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8cddeaa2d934e71e817f7dc57cefd1ed.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e595ac0692ae672cf3ea7a03e1e6ad6c.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_8cddeaa2d934e71e817f7dc57cefd1ed.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_e595ac0692ae672cf3ea7a03e1e6ad6c.msa index 2d37ed2b..eaecc408 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8cddeaa2d934e71e817f7dc57cefd1ed.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_e595ac0692ae672cf3ea7a03e1e6ad6c.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63964668-63966718 +>syndip_1_chr20:63964668-63966717 cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg aggag------------------------------------------------------- @@ -33,8 +33,8 @@ actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc -tccagctgggt ->syndip_2_chr20:63964668-63966718 +tccagctggg +>syndip_2_chr20:63964668-63966717 cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg @@ -69,8 +69,8 @@ actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc -tccagctgggt ->p:HG002_1_chr20:63964668-63966718 +tccagctggg +>p:HG002_1_chr20:63964668-63966717 cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg @@ -105,8 +105,8 @@ actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc -tccagctgggt ->p:HG002_2_chr20:63964668-63966718 +tccagctggg +>p:HG002_2_chr20:63964668-63966717 cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg aggag------------------------------------------------------- @@ -141,8 +141,8 @@ actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc -tccagctgggt ->ref_chr20:63964668-63966718 +tccagctggg +>ref_chr20:63964668-63966717 cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg @@ -177,4 +177,4 @@ actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc -tccagctgggt +tccagctggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8ac3ffdda713c1cb5ce15ef3970c84f1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e7315f7330dde260068b31e9e14647d0.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_8ac3ffdda713c1cb5ce15ef3970c84f1.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_e7315f7330dde260068b31e9e14647d0.msa index d04a37da..7b2e62c3 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8ac3ffdda713c1cb5ce15ef3970c84f1.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_e7315f7330dde260068b31e9e14647d0.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:53203887-53204574 +>syndip_1_chr20:53203887-53204573 cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc cttcatttttataatatgatactattatatcataattttataatatactattatatcata @@ -25,8 +25,8 @@ atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg -aaattccatgcatagctgacattctacttctattg ->syndip_2_chr20:53203887-53204574 +aaattccatgcatagctgacattctacttctatt +>syndip_2_chr20:53203887-53204573 cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc cttcatttttataatatgatactattatatcataattttataatatactattatatcata @@ -53,8 +53,8 @@ atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg -aaattccatgcatagctgacattctacttctattg ->p:HG002_1_chr20:53203887-53204574 +aaattccatgcatagctgacattctacttctatt +>p:HG002_1_chr20:53203887-53204573 cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc cttcatttttataatatgatactattatatcataattttataatatactattatatcata @@ -81,8 +81,8 @@ atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg -aaattccatgcatagctgacattctacttctattg ->p:HG002_2_chr20:53203887-53204574 +aaattccatgcatagctgacattctacttctatt +>p:HG002_2_chr20:53203887-53204573 cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc cttcatttttataatatgatactattatatcataattttataatatactattatatcata @@ -109,8 +109,8 @@ atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg -aaattccatgcatagctgacattctacttctattg ->ref_chr20:53203887-53204574 +aaattccatgcatagctgacattctacttctatt +>ref_chr20:53203887-53204573 cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc cttcatttttataatatgatactattatatcataattttataatatactattatatcata @@ -137,4 +137,4 @@ atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg -aaattccatgcatagctgacattctacttctattg +aaattccatgcatagctgacattctacttctatt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3a4684a9cebe728f709cb7d7bf349ea7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e98e8b7a2d661c3ba62b21a0dbc4f7d7.msa similarity index 87% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_3a4684a9cebe728f709cb7d7bf349ea7.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_e98e8b7a2d661c3ba62b21a0dbc4f7d7.msa index 7e9c806f..26a82542 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3a4684a9cebe728f709cb7d7bf349ea7.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_e98e8b7a2d661c3ba62b21a0dbc4f7d7.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:45600469-45600847 +>syndip_1_chr20:45600469-45600846 aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt @@ -8,8 +8,8 @@ tctctctctctccctctctctctctttctccctctctctccctctctctctctctctctc cctctctctctctttctccctctctctccctctctccccctctctctccctctctccctc tctccctctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc -catcataccagctcttcccctggtatattcctaggagtgga ->syndip_2_chr20:45600469-45600847 +catcataccagctcttcccctggtatattcctaggagtgg +>syndip_2_chr20:45600469-45600846 aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt @@ -19,8 +19,8 @@ tctctctctctccctctctct--------------------------------------- -------------------------------------ccctctctccccctctctctccc tctctccctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc -catcataccagctcttcccctggtatattcctaggagtgga ->p:HG002_1_chr20:45600469-45600847 +catcataccagctcttcccctggtatattcctaggagtgg +>p:HG002_1_chr20:45600469-45600846 aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt @@ -30,8 +30,8 @@ tctctctctctccctctctct--------------------------------------- -------------------------------------ccctctctccccctctctctccc tctctccctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc -catcataccagctcttcccctggtatattcctaggagtgga ->p:HG002_2_chr20:45600469-45600847 +catcataccagctcttcccctggtatattcctaggagtgg +>p:HG002_2_chr20:45600469-45600846 aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt @@ -41,8 +41,8 @@ tctctctctctccctctctctctctttctccctctctctccctctctctctctctctctc cctctctctctctttctccctctctctccctctctccccctctctctccctctctccctc tctccctctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc -catcataccagctcttcccctggtatattcctaggagtgga ->ref_chr20:45600469-45600847 +catcataccagctcttcccctggtatattcctaggagtgg +>ref_chr20:45600469-45600846 aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt @@ -52,4 +52,4 @@ aaaagcagtctctctctctctctctctctctctct------------------------- ---------------------------------------------------------ctc tatccccccctctccctctctctctacccctgaatctggcctttctaaacaccctcaact tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc -catcataccagctcttcccctggtatattcctaggagtgga +catcataccagctcttcccctggtatattcctaggagtgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fbbef252bd5883cf143b0f4c4649c512.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ed1042b42c059891aecf75a626d0d1a8.msa similarity index 98% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_fbbef252bd5883cf143b0f4c4649c512.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_ed1042b42c059891aecf75a626d0d1a8.msa index e6db8916..9504a597 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fbbef252bd5883cf143b0f4c4649c512.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_ed1042b42c059891aecf75a626d0d1a8.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:55943819-55945908 +>syndip_1_chr20:55943819-55945907 gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat @@ -36,8 +36,8 @@ ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca -tgggc ->syndip_2_chr20:55943819-55945908 +tggg +>syndip_2_chr20:55943819-55945907 gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat @@ -75,8 +75,8 @@ ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca -tgggc ->p:HG002_1_chr20:55943819-55945908 +tggg +>p:HG002_1_chr20:55943819-55945907 gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat @@ -114,8 +114,8 @@ ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca -tgggc ->p:HG002_2_chr20:55943819-55945908 +tggg +>p:HG002_2_chr20:55943819-55945907 gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat @@ -153,8 +153,8 @@ ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca -tgggc ->ref_chr20:55943819-55945908 +tggg +>ref_chr20:55943819-55945907 gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat @@ -192,4 +192,4 @@ ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca -tgggc +tggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_67fd23689620e3340fe2a29e2ea77933.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ed11e856d3a32487f771047b0b77f027.msa similarity index 96% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_67fd23689620e3340fe2a29e2ea77933.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_ed11e856d3a32487f771047b0b77f027.msa index fbf24462..156d29b9 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_67fd23689620e3340fe2a29e2ea77933.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_ed11e856d3a32487f771047b0b77f027.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:20320185-20320680 +>syndip_1_chr20:20320185-20320679 atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga tggtatttcagatatatag--atatatatattatatatatgtaatatatataatatatgt @@ -28,8 +28,8 @@ tatatattatatatattatatatgtaatatatattatatatattatatatgtaatatata ttatatatattatatatgtaatatatattatatatattatatatgtaatatatattatat atattatatatgtaatatatatatatttaaaaacagaaccattatcttttagagatacat actgaagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaact -agagatgacccaagactgcccttgagctaataactgt ->syndip_2_chr20:20320185-20320680 +agagatgacccaagactgcccttgagctaataactg +>syndip_2_chr20:20320185-20320679 atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt @@ -59,8 +59,8 @@ gaagtgtctggagacatgcttcaagata-------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------acccaggagggagaatggtagaaggaact -agagatgacccaagactgcccttgagctaataactgt ->p:HG002_1_chr20:20320185-20320680 +agagatgacccaagactgcccttgagctaataactg +>p:HG002_1_chr20:20320185-20320679 atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt @@ -90,8 +90,8 @@ gaagtgtctggagacatgcttcaagata-------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------acccaggagggagaatggtagaaggaact -agagatgacccaagactgcccttgagctaataactgt ->p:HG002_2_chr20:20320185-20320680 +agagatgacccaagactgcccttgagctaataactg +>p:HG002_2_chr20:20320185-20320679 atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga tggtatttcagatatatag--atatatatattatatatatgtaatatatataatatatgt @@ -121,8 +121,8 @@ tatatattatatatattatatatgtaatatatattatatatattatatatgtaatatata ttatatatattatatatgtaatatatattatatatattatatatgtaatatatattatat atattatatatgtaatatatatatatttaaaaacagaaccattatcttttagagatacat actgaagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaact -agagatgacccaagactgcccttgagctaataactgt ->ref_chr20:20320185-20320680 +agagatgacccaagactgcccttgagctaataactg +>ref_chr20:20320185-20320679 atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt @@ -152,4 +152,4 @@ gaagtgtctggagacatgcttcaagata-------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------acccaggagggagaatggtagaaggaact -agagatgacccaagactgcccttgagctaataactgt +agagatgacccaagactgcccttgagctaataactg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4891d56deb85c16ff9f7722808d6cd91.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_edce4871de28f10080aaa834a9139704.msa similarity index 91% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_4891d56deb85c16ff9f7722808d6cd91.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_edce4871de28f10080aaa834a9139704.msa index f4bd8df9..dca76d89 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4891d56deb85c16ff9f7722808d6cd91.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_edce4871de28f10080aaa834a9139704.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:62270179-62271195 +>syndip_1_chr20:62270179-62271194 cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg @@ -15,8 +15,8 @@ tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct -gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa ->syndip_2_chr20:62270179-62271195 +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtggga +>syndip_2_chr20:62270179-62271194 cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg @@ -33,8 +33,8 @@ tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct -gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa ->p:HG002_1_chr20:62270179-62271195 +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtggga +>p:HG002_1_chr20:62270179-62271194 cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg @@ -51,8 +51,8 @@ tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct -gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa ->p:HG002_2_chr20:62270179-62271195 +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtggga +>p:HG002_2_chr20:62270179-62271194 cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg @@ -69,8 +69,8 @@ tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct -gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgagaa ->ref_chr20:62270179-62271195 +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgaga +>ref_chr20:62270179-62271194 cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg @@ -87,4 +87,4 @@ tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct -gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa +gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtggga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_89449e11a504a87076c2d55f89a99cbd.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f421dd5eadc752e68b598f461ab861a8.msa similarity index 95% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_89449e11a504a87076c2d55f89a99cbd.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_f421dd5eadc752e68b598f461ab861a8.msa index df5fb594..faa3b7a3 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_89449e11a504a87076c2d55f89a99cbd.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_f421dd5eadc752e68b598f461ab861a8.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:23155404-23156076 +>syndip_1_chr20:23155404-23156075 gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc ctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggg @@ -14,8 +14,8 @@ gaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct -gcaaagccccca ->syndip_2_chr20:23155404-23156076 +gcaaagccccc +>syndip_2_chr20:23155404-23156075 gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg @@ -31,8 +31,8 @@ gaaagaaag------------------------aagaaagaaagaaagaaagaaagaaag aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct -gcaaagccccca ->p:HG002_1_chr20:23155404-23156076 +gcaaagccccc +>p:HG002_1_chr20:23155404-23156075 gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg @@ -48,8 +48,8 @@ gaaagaaag------------------------aagaaagaaagaaagaaagaaagaaag aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct -gcaaagccccca ->p:HG002_2_chr20:23155404-23156076 +gcaaagccccc +>p:HG002_2_chr20:23155404-23156075 gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc ctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggg @@ -65,8 +65,8 @@ gaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct -gcaaagccccca ->ref_chr20:23155404-23156076 +gcaaagccccc +>ref_chr20:23155404-23156075 gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg @@ -82,4 +82,4 @@ gaaagaaag------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaag aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct -gcaaagccccca +gcaaagccccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_85aa1e76d010d424a529fed9eb355830.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f5ab8103fdc862862724ddfcfe43644a.msa similarity index 97% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_85aa1e76d010d424a529fed9eb355830.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_f5ab8103fdc862862724ddfcfe43644a.msa index af467528..39e41974 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_85aa1e76d010d424a529fed9eb355830.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_f5ab8103fdc862862724ddfcfe43644a.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:61201583-61202575 +>syndip_1_chr20:61201583-61202574 aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccgtta gagaaggaatttcctcactcaggaccctctgcggatgtcacctccatcctcatcaggacc @@ -30,8 +30,8 @@ cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc -acctctctctcagactaggct ->syndip_2_chr20:61201583-61202575 +acctctctctcagactaggc +>syndip_2_chr20:61201583-61202574 aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc @@ -63,8 +63,8 @@ cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct aaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc -acctctctctcagactaggct ->p:HG002_1_chr20:61201583-61202575 +acctctctctcagactaggc +>p:HG002_1_chr20:61201583-61202574 aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc @@ -96,8 +96,8 @@ cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct aaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc -acctctctctcagactaggct ->p:HG002_2_chr20:61201583-61202575 +acctctctctcagactaggc +>p:HG002_2_chr20:61201583-61202574 aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccgtta gagaaggaatttcctcactcaggaccctctgcggatgtcacctccatcctcatcaggacc @@ -129,8 +129,8 @@ cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc -acctctctctcagactaggct ->ref_chr20:61201583-61202575 +acctctctctcagactaggc +>ref_chr20:61201583-61202574 aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc @@ -162,4 +162,4 @@ cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc -acctctctctcagactaggct +acctctctctcagactaggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_652adf9a4e7824ea572dca71a0562a04.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f80b3949aaede63b2c726a14abd6e835.msa similarity index 92% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_652adf9a4e7824ea572dca71a0562a04.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_f80b3949aaede63b2c726a14abd6e835.msa index d158507f..0379a39e 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_652adf9a4e7824ea572dca71a0562a04.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_f80b3949aaede63b2c726a14abd6e835.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:61289525-61290656 +>syndip_1_chr20:61289525-61290655 tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga @@ -17,8 +17,8 @@ gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg -cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc ->syndip_2_chr20:61289525-61290656 +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgc +>syndip_2_chr20:61289525-61290655 tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga @@ -37,8 +37,8 @@ gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg -cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc ->p:HG002_1_chr20:61289525-61290656 +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgc +>p:HG002_1_chr20:61289525-61290655 tctgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga @@ -57,8 +57,8 @@ gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg -cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc ->p:HG002_2_chr20:61289525-61290656 +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgc +>p:HG002_2_chr20:61289525-61290655 tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga @@ -77,8 +77,8 @@ gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca cagaggaaattgatggcttggcagacagcgtgacatgttgactacctgccctggtccttg -cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc ->ref_chr20:61289525-61290656 +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgc +>ref_chr20:61289525-61290655 tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga @@ -97,4 +97,4 @@ gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg -cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgcc +cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_72f8e0bf8162cc30b5455b515c643479.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fb52ef3187571c67509303c4c8e9c08d.msa similarity index 93% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_72f8e0bf8162cc30b5455b515c643479.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_fb52ef3187571c67509303c4c8e9c08d.msa index 09fa7e28..d35585ef 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_72f8e0bf8162cc30b5455b515c643479.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_fb52ef3187571c67509303c4c8e9c08d.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:41196110-41196749 +>syndip_1_chr20:41196110-41196748 agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa @@ -12,8 +12,8 @@ tatatattatatattataaatatatattatatattatatattatataaatattatatata atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca -aagtgaaggctttgaaggcca ->syndip_2_chr20:41196110-41196749 +aagtgaaggctttgaaggcc +>syndip_2_chr20:41196110-41196748 agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa @@ -27,8 +27,8 @@ tatataatatatattataaatatatattatatattatatattatataaatattatatata atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca -aagtgaaggctttgaaggcca ->p:HG002_1_chr20:41196110-41196749 +aagtgaaggctttgaaggcc +>p:HG002_1_chr20:41196110-41196748 agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa @@ -42,8 +42,8 @@ tatataatatatattataaatatatattatatattatatattatataaatattatatata atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca -aagtgaaggctttgaaggcca ->p:HG002_2_chr20:41196110-41196749 +aagtgaaggctttgaaggcc +>p:HG002_2_chr20:41196110-41196748 agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa @@ -57,8 +57,8 @@ tatatattatatattataaatatatattatatattatatattatataaatattatatata atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca -aagtgaaggctttgaaggcca ->ref_chr20:41196110-41196749 +aagtgaaggctttgaaggcc +>ref_chr20:41196110-41196748 agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa @@ -72,4 +72,4 @@ atattatatataatatatttatatataatatatatttatatattataaatatatat---- atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca -aagtgaaggctttgaaggcca +aagtgaaggctttgaaggcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8f331d26b3bb88ff009d81b04c1c6f26.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fc40819c3b411d6b2869794670b475f9.msa similarity index 87% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_8f331d26b3bb88ff009d81b04c1c6f26.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_fc40819c3b411d6b2869794670b475f9.msa index 950ef9f8..9d83252e 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8f331d26b3bb88ff009d81b04c1c6f26.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_fc40819c3b411d6b2869794670b475f9.msa @@ -1,40 +1,40 @@ ->syndip_1_chr20:60702905-60703188 +>syndip_1_chr20:60702905-60703187 attttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatt tgtcattgtctttctttcttttctttctctctctctctttcttttccttctttctttctt tctttctttctttctttctttctttctttctttctttctttcttttctttccttcttctt tctttctttctttctttctttctttctttctttctttctttctttctttctttctttctt tctttctttctttcttctttctttctttttctttcttttttttttgggatggagtctcgc tctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacctccc -aggttcaagcgattgaa ->syndip_2_chr20:60702905-60703188 +aggttcaagcgattga +>syndip_2_chr20:60702905-60703187 attttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatt tgtcattgtctttctttcttttctttctctctctctctttcttttccttctttctttctt tctttctttctttcttc----------------------------------------ctt tctttctttctttctttctttctttctttctttctttcttt------------------- ------tctttccttctttctttctttctttctttctttttttttgggatggagtctcgc tctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacctccc -aggttcaagcgattgaa ->p:HG002_1_chr20:60702905-60703188 +aggttcaagcgattga +>p:HG002_1_chr20:60702905-60703187 attttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatt tgtcattgtctttctttcttttctttctctctctctctttctttcttttccttctttctt tctttctttctttcctt----------------------------------------ctt tctttctttctttctttctttctttctttctttctttcttt------------------- ------tctttccttctttctttctttctttctttctttttttttgggatggagtctcgc tctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacctccc -aggttcaagcgattgaa ->p:HG002_2_chr20:60702905-60703188 +aggttcaagcgattga +>p:HG002_2_chr20:60702905-60703187 attttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatt tgtcattgtctttctttcttttctttctctctctctctttcttttccttctttctttctt tctttctttctttctttctttctttctttctttctttctttcttttctttccttcttctt tctttctttctttctttctttctttctttctttctttctttctttctttctttctttctt tctttctttctttcttcttctttctttctttctttctttttttttgggatggagtctcgc tctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacctccc -aggttcaagcgattgaa ->ref_chr20:60702905-60703188 +aggttcaagcgattga +>ref_chr20:60702905-60703187 attttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatt tgtcattgtctttctttcttttctttctctctctctctttcttttcctt----------- ---------------------------------------------------------ctt tctttctttctttctttctttctttctttctttctttcttt------------------- ------tctttccttctttctttctttctttctttctttttttttgggatggagtctcgc tctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacctccc -aggttcaagcgattgaa +aggttcaagcgattga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_79d4b9c2180cea7a5edfdeebbbf56834.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fd198272bc91bdb42e2dbb32cc9c9935.msa similarity index 99% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_79d4b9c2180cea7a5edfdeebbbf56834.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_fd198272bc91bdb42e2dbb32cc9c9935.msa index c27b67dc..d7d2eb13 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_79d4b9c2180cea7a5edfdeebbbf56834.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_fd198272bc91bdb42e2dbb32cc9c9935.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63167287-63167728 +>syndip_1_chr20:63167287-63167727 aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcacggt tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc @@ -74,8 +74,8 @@ ccccacctcagcccccacctccgcccccacctcagcccctcctcagcccccacctctgcc cccacctcagaccctcctcagcccctcctcagcccctcctcatcccctcctcagcagctg ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg -ccttgt ->syndip_2_chr20:63167287-63167728 +ccttg +>syndip_2_chr20:63167287-63167727 aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg ctatccatcccctcgactaatacttaccaaattaattccagatttggattcactcacggt tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc @@ -151,8 +151,8 @@ cccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgcc cccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagctg ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg -ccttgt ->p:HG002_1_chr20:63167287-63167728 +ccttg +>p:HG002_1_chr20:63167287-63167727 aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg ctatccatcccctcgactaatacttaccaaattaattccagatttggattcactcacggt tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc @@ -228,8 +228,8 @@ cccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgcc cccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagctg ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg -ccttgt ->p:HG002_2_chr20:63167287-63167728 +ccttg +>p:HG002_2_chr20:63167287-63167727 aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcacggt tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc @@ -305,8 +305,8 @@ ccccacctcagcccccacctccgcccccacctcagcccctcctcagcccccacctctgcc cccacctcagaccctcctcagcccctcctcagcccctcctcatcccctcctcagcagctg ctggaatgggctaccctcaggagttggcaccccacagcctccttcccttcccacctccgc cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg -ccttgt ->ref_chr20:63167287-63167728 +ccttg +>ref_chr20:63167287-63167727 aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcatggt tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc @@ -382,4 +382,4 @@ agtgcccacctcagccccctcctcagccccca---------------------------- cccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagctg ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg -ccttgt +ccttg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fdcb2c8d04f052ec0422554bbca6ba2d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fdcb2c8d04f052ec0422554bbca6ba2d.msa new file mode 100644 index 00000000..761b2923 --- /dev/null +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_fdcb2c8d04f052ec0422554bbca6ba2d.msa @@ -0,0 +1,165 @@ +>syndip_1_chr20:60314230-60315120 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttgtccttccttccttccttccttccttc---cttccttccttccttccttccttcc +ttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacc +atcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatcc +atccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatcc +atcctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatcc +actcttccatccatccatccacccaccctt----------------ccatccatccatcc +tcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatcc +atcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcc +tcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatccatcc +tcccatcctcccatccatccatccatcctcccatccgtccatccatccttccatccac-- +--------------cctcccatccatccatcctcccatccatctaccctcccatccatcc +atcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatct +atccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcct +cccataatctatcttcccatccatttgtccttccttccttccttccttccttccttcctt +cgttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaa +ccatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctat +ccat--------------------ccatcctcccatccatcctcccatcctcccatccat +tctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctc +ccatccatccatcctcccatccatccacccttccatccatccatccacccacccttccat +ccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctc +ccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccat +ccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccat +ccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccat +cctcccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccat +cgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccat +ccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccat +ccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgt +gagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaa +aatgaaaaaaagaatatattgatttcaggccagttacatag +>syndip_2_chr20:60314230-60315120 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttg--------------------tccttc---cttccttccttccttccttccttcc +ttccacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaacc +atcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatcc +atccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatcc +atcctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatcc +acccttccatccatccatccacccacccttccatccatccatcctcccatccatccatcc +tcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatcc +atcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcc +tcccatccatctaccctcccatccatccatcctcccatccaccctcccatccatccatcc +atccatccaccctctcatccatccatcctcccatccgtccatccatccttccatccaccc +tcccatccatccatcctcccatccatccatcctcccatccatctaccctcccatccatcc +atcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatct +atccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcct +cccataatctatcttcccatccatttgtccttccttccttccttccttccttcc------ +--ttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaa +ccatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctat +ccatccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatccat +tctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctc +ccatccatccatcctcccatccatccacccttccatccatccatccacccacccttccat +ccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctc +ccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccat +ccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccat +ccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccat +cctc----ccatccatccatccatccatccatcctcccatcctcccatcctcccatccat +cgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccat +ccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccat +ccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgt +gagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaa +aatgaaaaaaagaatatattgatttcaggccagttacatag +>p:HG002_1_chr20:60314230-60315120 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttg--------------------tccttc---cttccttccttccttccttccttcc +ttccacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaacc +atcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatcc +atccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatcc +atcctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatcc +acccttccatccatccatccacccacccttccatccatccatcctcccatccatccatcc +tcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatcc +atcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcc +tcccatccatctaccctcccatccatccatcctcccatccaccctcccatccatccatcc +atccatccaccctctcatccatccatcctcccatccgtccatccatccttccatccaccc +tcccatccatccatcctcccatccatccatcctcccatccatctaccctcccatccatcc +atcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatct +atccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcct +cccataatctatcttcccatccatttgtccttccttccttccttccttccttcc------ +--ttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaa +ccatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctat +ccatccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatccat +tctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctc +ccatccatccatcctcccatccatccacccttccatccatccatccacccacccttccat +ccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctc +ccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccat +ccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccat +ccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccat +cctc----ccatccatccatccatccatccatcctcccatcctcccatcctcccatccat +cgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccat +ccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccat +ccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgt +gagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaa +aatgaaaaaaagaatatattgatttcaggccagttacatag +>p:HG002_2_chr20:60314230-60315120 +acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac +acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt +cctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc +catttgtccttccttccttccttccttccttc---cttccttccttccttccttccttcc +ttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacc +atcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatcc +atccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatcc +atcctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatcc +actcttccatccatccatccacccaccctt----------------ccatccatccatcc +tcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatcc +atcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcc +tcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatccatcc +tcccatcctcccatccatccatccatcctcccatccgtccatccatccttccatccac-- +--------------cctcccatccatccatcctcccatccatctaccctcccatccatcc +atcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatct +atccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcct +cccataatctatcttcccatccatttgtccttccttccttccttccttccttccttcctt +cgttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaa +ccatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctat +ccat--------------------ccatcctcccatccatcctcccatcctcccatccat +tctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctc +ccatccatccatcctcccatccatccacccttccatccatccatccacccacccttccat +ccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctc +ccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccat +ccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccat +ccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccat 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+tccacctccaccaccaccaccaccacctccactaccaccacctccacctccaccaccacc +acctccaccaccaacacctccacctccacctccacctccaccaccaccacctccacctcc +accaccaccacctccaccaccaccacctccaccacctccacctccaccaccaccacctcc +accaccacctccaccaccaccaccacctccaccaccaccacctccaccaccacctccacc +accaccacctccaccaccacctccaccaccacctccacctccaccaccaccacctgcacc +accacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcacttgt +tggggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgacccctaa +gcacagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctggggggtca +actgcacacgccagggtcctagggtcctagacccctgtcctccctgtttctgcctctgtt +tggggtggagtccaagtct +>ref_chr20:63693225-63693984 +tcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactgg +taaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagt +cctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccct +atgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacct-- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------ccacctccacct----------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------------ccacc +tccaccaccacctccacctccaccaccacctcctccaccaccaccacctccaccaccacc +accaccaccaccacctccacctccaccacctccacctccaccaccaccacctccacct-- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------ccaccaccacc +acctccacctccaccaccacctccaccaccaccacctccacctccacca----------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------ccacctccacc +accaccaccaccaccaccaccaccaccacca----------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------ccacctccaccaccaccacctgcacc +accacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcacttgt +tggggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgacccctaa +gcacagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctggggggtca +actgcacacgccagggtcctagggtcctagacccctgtcctccctgtttctgcctctgtt +tggggtggagtccaagtct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0e637d93ff26bf168ee302bf13d84ca8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ff5bbed9fc29f7f0637d3929908a94a3.msa similarity index 90% rename from repo_utils/test_files/external/fake_mafft/lookup/fm_0e637d93ff26bf168ee302bf13d84ca8.msa rename to repo_utils/test_files/external/fake_mafft/lookup/fm_ff5bbed9fc29f7f0637d3929908a94a3.msa index b9fb50de..25f289a0 100644 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0e637d93ff26bf168ee302bf13d84ca8.msa +++ b/repo_utils/test_files/external/fake_mafft/lookup/fm_ff5bbed9fc29f7f0637d3929908a94a3.msa @@ -1,4 +1,4 @@ ->syndip_1_chr20:63641679-63642236 +>syndip_1_chr20:63641679-63642235 tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca @@ -13,8 +13,8 @@ gccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctcc gagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt -tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg ->syndip_2_chr20:63641679-63642236 +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgt +>syndip_2_chr20:63641679-63642235 tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca @@ -29,8 +29,8 @@ tccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctcc gagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc ccggcccctgcccgctccgaactccgccccggccccgcccccgcaccttctcgcgcagcc gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt -tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg ->p:HG002_1_chr20:63641679-63642236 +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgt +>p:HG002_1_chr20:63641679-63642235 tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc tgctggggacgcccagtaaacacgggaggagcccccgatccccaccccagctcagcgcct cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca @@ -45,8 +45,8 @@ tccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctcc gagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc ccggcccctgcccgctccgaactccgccccggccccgcccccgcaccttctcgcgcagcc gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt -tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg ->p:HG002_2_chr20:63641679-63642236 +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgt +>p:HG002_2_chr20:63641679-63642235 tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca @@ -61,8 +61,8 @@ gccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctcc gagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt -tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg ->ref_chr20:63641679-63642236 +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgt +>ref_chr20:63641679-63642235 tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca @@ -77,4 +77,4 @@ cgcccagtgccccgccccctgactgctgctagccctgc---------------------- --------------ccccgccccggcccctgcccgctccgagcttcgccccggccccgcc ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt -tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg +tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgt diff --git a/truvari/refine.py b/truvari/refine.py index cadc7132..bd2947be 100644 --- a/truvari/refine.py +++ b/truvari/refine.py @@ -150,7 +150,7 @@ def refined_stratify(outdir, to_eval_coords, regions, threads=1): regions = regions.join(counts) for i in ["tpbase", "tp", "fn", "fp"]: regions[f"out_{i}"] = regions[f"in_{i}"].where( - ~regions['refined'], regions[f"out_{i}"]) + ~regions['refined'], regions[f"out_{i}"]).infer_objects(copy=False) return regions From f07975e3f809d80e79514824517128a2e3f0c1ef Mon Sep 17 00:00:00 2001 From: Adam English Date: Mon, 5 Feb 2024 17:07:55 -0500 Subject: [PATCH 7/8] preparing command --- imgs/coverage.svg | 4 +- .../ga4gh/ga4gh_norefine_query.vcf.gz | Bin 0 -> 38090 bytes .../ga4gh/ga4gh_norefine_truth.vcf.gz | Bin 0 -> 32052 bytes .../ga4gh/ga4gh_withrefine_query.vcf.gz | Bin 0 -> 33851 bytes .../ga4gh/ga4gh_withrefine_truth.vcf.gz | Bin 0 -> 27510 bytes repo_utils/answer_key/help.txt | 5 +- repo_utils/sub_tests/ga4gh.sh | 16 ++ truvari/__init__.py | 2 +- truvari/__main__.py | 3 + truvari/make_ga4gh.py | 209 ++++++++++++++++++ truvari/msatovcf.py | 2 +- 11 files changed, 235 insertions(+), 6 deletions(-) create mode 100644 repo_utils/answer_key/ga4gh/ga4gh_norefine_query.vcf.gz create mode 100644 repo_utils/answer_key/ga4gh/ga4gh_norefine_truth.vcf.gz create mode 100644 repo_utils/answer_key/ga4gh/ga4gh_withrefine_query.vcf.gz create mode 100644 repo_utils/answer_key/ga4gh/ga4gh_withrefine_truth.vcf.gz create mode 100644 repo_utils/sub_tests/ga4gh.sh create mode 100644 truvari/make_ga4gh.py diff --git a/imgs/coverage.svg b/imgs/coverage.svg index ea71b13a..4421b8a1 100644 --- a/imgs/coverage.svg +++ b/imgs/coverage.svg @@ -17,7 +17,7 @@ coverage - 90% - 90% + 88% + 88% diff --git a/repo_utils/answer_key/ga4gh/ga4gh_norefine_query.vcf.gz b/repo_utils/answer_key/ga4gh/ga4gh_norefine_query.vcf.gz new file mode 100644 index 0000000000000000000000000000000000000000..9defc9d8e9ad250083c2d96359fccc2ed1fb0875 GIT binary patch literal 38090 zcmV)AK*YZviwFb&00000{{{d;LjnNXA?-bBbK6FipEbXNJNdAg+KB4=uvc4!z&7HY z*zwrd%+4nlEzvS-B+(<%PBK&b-?tAm&_EvqNlA2E(#by2ct`i^*YCal=9~A6%lZ4| z&DCsu`g8g0Gnv9aeDlq-=Rej@U!VTx^CzdTiZ^e*doo|0-7G$?7t8C@KNgpl6V+-x zzgbN_&Q`1W`5*sFwK-c}uNN1l&Dn<=_}%6F`eOaz6cHgQBM60cP*(>*i7Ap{9qj5r 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-Truvari v4.3.0.dev Structural Variant Benchmarking and Annotation +Truvari v4.2.1.dev Structural Variant Benchmarking and Annotation Available commands: bench Performance metrics from comparison of two VCFs @@ -13,12 +13,13 @@ Available commands: divide Divide a VCF into independent shards phab Variant harmonization using MSA refine Automated bench result refinement with phab + ga4gh Convert Truvari result to GA4GH version Print the Truvari version and exit positional arguments: CMD Command to execute OPTIONS Options to pass to the command -options: +optional arguments: -h, --help show this help message and exit diff --git a/repo_utils/sub_tests/ga4gh.sh b/repo_utils/sub_tests/ga4gh.sh new file mode 100644 index 00000000..3484496d --- /dev/null +++ b/repo_utils/sub_tests/ga4gh.sh @@ -0,0 +1,16 @@ +# ------------------------------------------------------------ +# ga4gh +# ------------------------------------------------------------ +run test_ga4gh $truv ga4gh -i $ANSDIR/refine/refine_output_three/ -o $OD/ga4gh_norefine +if [ $test_ga4gh ]; then + assert_exit_code 0 + assert_equal $(fn_md5 $ANSDIR/ga4gh/ga4gh_norefine_truth.vcf.gz) $(fn_md5 $OD/ga4gh_norefine_truth.vcf.gz) + assert_equal $(fn_md5 $ANSDIR/ga4gh/ga4gh_norefine_query.vcf.gz) $(fn_md5 $OD/ga4gh_norefine_query.vcf.gz) +fi + +run test_ga4gh_refine $truv ga4gh -w -i $ANSDIR/refine/refine_output_three/ -o $OD/ga4gh_withrefine +if [ $test_ga4gh ]; then + assert_exit_code 0 + assert_equal $(fn_md5 $ANSDIR/ga4gh/ga4gh_withrefine_truth.vcf.gz) $(fn_md5 $OD/ga4gh_withrefine_truth.vcf.gz) + assert_equal $(fn_md5 $ANSDIR/ga4gh/ga4gh_withrefine_query.vcf.gz) $(fn_md5 $OD/ga4gh_withrefine_query.vcf.gz) +fi diff --git a/truvari/__init__.py b/truvari/__init__.py index c0506d64..e954b270 100644 --- a/truvari/__init__.py +++ b/truvari/__init__.py @@ -88,7 +88,7 @@ :data:`truvari.SZBINTYPE` """ -__version__ = '4.3.0.dev' +__version__ = '4.2.1.dev' from truvari.annotations.af_calc import ( diff --git a/truvari/__main__.py b/truvari/__main__.py index 0b0a138c..e079d05e 100755 --- a/truvari/__main__.py +++ b/truvari/__main__.py @@ -20,6 +20,7 @@ from truvari.stratify import stratify_main from truvari.segmentation import segment_main from truvari.consistency import consistency_main +from truvari.make_ga4gh import make_ga4gh_main def flat_version(args): """Print the version""" @@ -39,6 +40,7 @@ def flat_version(args): "divide": divide_main, "phab": phab_main, "refine": refine_main, + "ga4gh": make_ga4gh_main, "version": flat_version} USAGE = f"""\ @@ -55,6 +57,7 @@ def flat_version(args): [bold][cyan]divide[/][/] Divide a VCF into independent shards [bold][cyan]phab[/][/] Variant harmonization using MSA [bold][cyan]refine[/][/] Automated bench result refinement with phab + [bold][cyan]ga4gh[/][/] Convert Truvari result to GA4GH [bold][cyan]version[/][/] Print the Truvari version and exit """ diff --git a/truvari/make_ga4gh.py b/truvari/make_ga4gh.py new file mode 100644 index 00000000..7d5704d9 --- /dev/null +++ b/truvari/make_ga4gh.py @@ -0,0 +1,209 @@ +""" +Consolidate truvari by truth/query and annotate with GA4GH intermediates tags +""" +import os +import sys +import json +import logging +import argparse +from collections import defaultdict + +import pysam +import pandas as pd +from intervaltree import IntervalTree + +import truvari + +def parse_args(args): + """ + Argument parser + """ + parser = argparse.ArgumentParser(prog="ga4gh", description=__doc__, + formatter_class=argparse.RawDescriptionHelpFormatter) + parser.add_argument("-i", "--input", required=True, + help="Truvari result directory") + parser.add_argument("-o", "--output", required=True, + help="Output suffix") + parser.add_argument("-w", "--with-refine", action="store_true", + help="Consolidate with `truvari refine` output") + parser.add_argument("-B", "--buffer", type=int, default=100, + help="Buffer length used by phab during refine (100)") + parser.add_argument("-b", "--bSample", default=0, + help="Sample name to annotate in truth VCF (default first)") + parser.add_argument("-c", "--cSample", default=0, + help="Sample name to annotate in query VCF (default first)") + + args = parser.parse_args(args) + return args + +def edit_header(header): + """ + Add INFO for new fields to vcf + """ + header.add_line(('##INFO=')) + header.add_line(('##FORMAT=')) + header.add_line(('##FORMAT=')) + return header + +def in_tree(tree, entry): + """ + return True if entry within boundaries of tree interval + """ + astart, aend = truvari.entry_boundaries(entry) + # Filter these early so we don't have to keep checking overlaps + if astart == aend - 1: + return tree[entry.chrom].overlaps(astart) + m_ovl = tree[entry.chrom].overlap(astart, aend) + if len(m_ovl) != 1: + return False + m_ovl = list(m_ovl)[0] + # Edge case - the variant spans the entire include region + return astart >= m_ovl.begin and aend <= m_ovl.end + +def build_tree(regions, buffer=0): + """ + Build tree from regions + """ + tree = defaultdict(IntervalTree) + for _, i in regions.iterrows(): + tree[i['chrom']].addi(i['start'] - buffer, i['end'] + buffer + 1) + for i in tree: + tree[i].merge_overlaps() + return tree + +def get_truvari_filenames(in_dir): + """ + Join in_dir to relevant filenames + """ + return {'tp-base': os.path.join(in_dir, 'tp-base.vcf.gz'), + 'tp-comp': os.path.join(in_dir, 'tp-comp.vcf.gz'), + 'fn': os.path.join(in_dir, 'fn.vcf.gz'), + 'fp': os.path.join(in_dir, 'fp.vcf.gz'), + 'params': os.path.join(in_dir, 'params.json')} + + +def move_record(entry, out_vcf, sample): + """ + Move the new entry (with the single specified sample) + to be writeable to the out_vcf + """ + ret = out_vcf.new_record(contig=entry.contig, start=entry.start, stop=entry.stop, alleles=entry.alleles, + id=entry.id, qual=entry.qual, filter=entry.filter, info=entry.info) + for k,v in entry.samples[sample].items(): + ret.samples[0][k] = v + return ret + +def parse_bench_dir(in_dir, t_vcf, q_vcf, tree, is_refined): + """ + Pull relevant entries from relevant files + """ + in_vcfs = get_truvari_filenames(in_dir) + params = None + with open(in_vcfs['params'], 'r') as fh: + params = json.load(fh) + bsamp = params['bSample'] + csamp = params['cSample'] + ops_to_do = [("tp-base", "TP", t_vcf, bsamp), ("fn", "FN", t_vcf, bsamp), + ("tp-comp", "TP", q_vcf, csamp), ("fp", "FP", q_vcf, csamp)] + for filename, bdkey, out_vcf, samp in ops_to_do: + m_vcf = pysam.VariantFile(in_vcfs[filename]) + m_iter = m_vcf if tree is None else truvari.region_filter(m_vcf, tree, is_refined) + for entry in m_iter: + n_entry = move_record(entry, out_vcf, samp) + n_entry.info["IsRefined"] = is_refined + n_entry.samples[0]["BD"] = bdkey + if bdkey.startswith('T'): + n_entry.samples[0]["BK"] = 'gm' if entry.info["GTMatch"] == 0 else 'am' + else: + n_entry.samples[0]["BK"] = '.' if entry.info["TruScore"] is None else 'lm' + out_vcf.write(n_entry) + +def check_bench_dir(dirname): + """ + Make sure all the files are there + """ + check_fail = False + b_files = get_truvari_filenames(dirname) + for k, v in b_files.items(): + if not os.path.exists(v): + logging.error("%s bench file doesn't exist", k) + check_fail = True + return check_fail + + +def check_args(args): + """ + Ensure everything we're looking for is available + return True if check failed + """ + check_fail = False + if not os.path.isdir(args.input): + logging.error("input is not a directory") + check_fail = True + else: + check_fail |= check_bench_dir(args.input) + + if os.path.exists(args.output + '_truth.vcf.gz'): + logging.error("%s_truth.vcf.gz already exists", args.output) + check_fail = True + if os.path.exists(args.output + '_truth.vcf.gz.tbi'): + logging.error("%s_truth.vcf.gz.tbi already exists", args.output) + check_fail = True + if os.path.exists(args.output + '_query.vcf.gz'): + logging.error("%s_query.vcf.gz already exists", args.output) + check_fail = True + if os.path.exists(args.output + '_query.vcf.gz.tbi'): + logging.error("%s_query.vcf.gz.tbi already exists", args.output) + check_fail = True + + if not args.with_refine: + return check_fail + + pdir = os.path.join(args.input, 'phab_bench') + if not os.path.exists(pdir): + logging.error("phab_bench dir doesn't exist") + check_fail = True + else: + check_fail |= check_bench_dir(pdir) + + return check_fail + +def make_ga4gh_main(args): + """ + Main entrypoint + """ + args = parse_args(args) + truvari.setup_logging() + + if check_args(args): + logging.error("Unable to do conversion") + sys.exit(1) + + logging.info("Consolidating VCFs") + + bench_vcfs = get_truvari_filenames(args.input) + + b_header = edit_header(pysam.VariantFile(bench_vcfs['tp-base'], 'r').header.copy()) + t_vcf_fn = args.output + '_truth.vcf' + t_vcf = pysam.VariantFile(t_vcf_fn, 'w', header=b_header) + + c_header = edit_header(pysam.VariantFile(bench_vcfs['tp-comp'], 'r').header.copy()) + q_vcf_fn = args.output + '_query.vcf' + q_vcf = pysam.VariantFile(q_vcf_fn, 'w', header=c_header) + + refine_tree = None + if args.with_refine: + regions = pd.read_csv(os.path.join(args.input, "refine.regions.txt"), sep='\t') + refine_tree = build_tree(regions[regions['refined']], args.buffer) + parse_bench_dir(os.path.join(args.input, 'phab_bench'), t_vcf, q_vcf, + tree=refine_tree, is_refined=True) + + parse_bench_dir(args.input, t_vcf, q_vcf, tree=refine_tree, is_refined=False) + t_vcf.close() + q_vcf.close() + truvari.compress_index_vcf(t_vcf_fn) + truvari.compress_index_vcf(q_vcf_fn) + logging.info("Finished") diff --git a/truvari/msatovcf.py b/truvari/msatovcf.py index 6224d9fc..c4b18619 100644 --- a/truvari/msatovcf.py +++ b/truvari/msatovcf.py @@ -142,7 +142,7 @@ def msa2vcf(msa, anchor_base='N'): >>> import truvari >>> from truvari.phab import fasta_reader >>> msa_dir = "repo_utils/test_files/external/fake_mafft/lookup/" - >>> msa_file = "fm_ca43b50e2a5d770bb34202d8a7b62421.msa" + >>> msa_file = "fm_7bb50c57d657828978076072c80f8a1f.msa" >>> seqs = open(msa_dir + msa_file).read() >>> fasta = dict(fasta_reader(seqs)) >>> m_entries_str = truvari.msa2vcf(fasta) From a7d0c027d6211611bd56a4072e762f67c468708d Mon Sep 17 00:00:00 2001 From: Adam English Date: Mon, 5 Feb 2024 17:23:11 -0500 Subject: [PATCH 8/8] finishing testing --- imgs/coverage.svg | 4 ++-- repo_utils/answer_key/help.txt | 2 +- repo_utils/sub_tests/ga4gh.sh | 7 ++++++- repo_utils/truvari_ssshtests.sh | 1 + truvari/make_ga4gh.py | 15 --------------- 5 files changed, 10 insertions(+), 19 deletions(-) diff --git a/imgs/coverage.svg b/imgs/coverage.svg index 4421b8a1..ea71b13a 100644 --- a/imgs/coverage.svg +++ b/imgs/coverage.svg @@ -17,7 +17,7 @@ coverage - 88% - 88% + 90% + 90% diff --git a/repo_utils/answer_key/help.txt b/repo_utils/answer_key/help.txt index 4a2f8289..974ea7d8 100644 --- a/repo_utils/answer_key/help.txt +++ b/repo_utils/answer_key/help.txt @@ -20,6 +20,6 @@ positional arguments: CMD Command to execute OPTIONS Options to pass to the command -optional arguments: +options: -h, --help show this help message and exit diff --git a/repo_utils/sub_tests/ga4gh.sh b/repo_utils/sub_tests/ga4gh.sh index 3484496d..40acc802 100644 --- a/repo_utils/sub_tests/ga4gh.sh +++ b/repo_utils/sub_tests/ga4gh.sh @@ -9,8 +9,13 @@ if [ $test_ga4gh ]; then fi run test_ga4gh_refine $truv ga4gh -w -i $ANSDIR/refine/refine_output_three/ -o $OD/ga4gh_withrefine -if [ $test_ga4gh ]; then +if [ $test_ga4gh_refine ]; then assert_exit_code 0 assert_equal $(fn_md5 $ANSDIR/ga4gh/ga4gh_withrefine_truth.vcf.gz) $(fn_md5 $OD/ga4gh_withrefine_truth.vcf.gz) assert_equal $(fn_md5 $ANSDIR/ga4gh/ga4gh_withrefine_query.vcf.gz) $(fn_md5 $OD/ga4gh_withrefine_query.vcf.gz) fi + +run test_ga4gh_badparam $truv ga4gh -w -i notreal.file1234 -o $ANSDIR/ga4gh/ga4gh_withrefine +if [ $test_ga4gh_badparam ]; then + assert_exit_code 1 +fi diff --git a/repo_utils/truvari_ssshtests.sh b/repo_utils/truvari_ssshtests.sh index 3e5cffa5..045fcd1c 100644 --- a/repo_utils/truvari_ssshtests.sh +++ b/repo_utils/truvari_ssshtests.sh @@ -19,6 +19,7 @@ source $TESTSRC/sub_tests/consistency.sh source $TESTSRC/sub_tests/divide.sh source $TESTSRC/sub_tests/doctests.sh source $TESTSRC/sub_tests/entry_main.sh +source $TESTSRC/sub_tests/ga4gh.sh source $TESTSRC/sub_tests/phab.sh source $TESTSRC/sub_tests/refine.sh source $TESTSRC/sub_tests/segment.sh diff --git a/truvari/make_ga4gh.py b/truvari/make_ga4gh.py index 7d5704d9..3df8a789 100644 --- a/truvari/make_ga4gh.py +++ b/truvari/make_ga4gh.py @@ -48,21 +48,6 @@ def edit_header(header): 'Description="Sub-type for decision (match/mismatch type) lm variants had any counterpart to which it could compare">')) return header -def in_tree(tree, entry): - """ - return True if entry within boundaries of tree interval - """ - astart, aend = truvari.entry_boundaries(entry) - # Filter these early so we don't have to keep checking overlaps - if astart == aend - 1: - return tree[entry.chrom].overlaps(astart) - m_ovl = tree[entry.chrom].overlap(astart, aend) - if len(m_ovl) != 1: - return False - m_ovl = list(m_ovl)[0] - # Edge case - the variant spans the entire include region - return astart >= m_ovl.begin and aend <= m_ovl.end - def build_tree(regions, buffer=0): """ Build tree from regions