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Bed processing improvements #26

Merged
merged 31 commits into from
Nov 7, 2022
Merged

Bed processing improvements #26

merged 31 commits into from
Nov 7, 2022
+309 −117

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milkschen
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@milkschen milkschen commented Nov 4, 2022 •
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  • Add a bed_isec_threshold (-B) option to adjust the bed intersection strategy. E.g., only intervals with >x% overlap (wrt the query) or >y bp overlap is considered as intersected
  • Add bed_test.cpp (some tests were moved from leviosam_test.cpp)
  • Update reconcile.cpp to remove the use of deprecated std::random_shuffle()
  • Add reconcile_test.cpp

@milkschen
v0.3.0
88d351a
@milkschen
minor formatting
8f47e29
@milkschen
formatting
2b8758f
@milkschen
realign all reads instead of only primary
97ee6f9
@milkschen
replace first and last CIGAR op with SCLIP if INS
300f0d0
@milkschen
formatting and docstrings
d4bc5a8
@milkschen
Merge branch 'main' into dev
d2508ea
@milkschen
vscode formatting
e302942
@milkschen
resolve conflicts
664ee42
@milkschen
indent =4
fa6c2b9
@milkschen
fix a warning
ecf13fc
@milkschen
formatting
a51a6ab
@milkschen
v0.3.0
ee39887
@milkschen
formatting
1ff7313
@milkschen
Merge branch 'dev' of github.com:milkschen/leviosam2 into dev
864ee21
@milkschen
test file for bed
11961c5
@milkschen
Merge branch 'main' into dev
adb22e2
@milkschen
move to bed_test
9336acd
@milkschen
test
b62dabe
@milkschen
bed_test
f60b6e5
@milkschen
consider fraction/size of an interval overlap
3d52c0d
@milkschen
docstring
0e8232a
@milkschen
stop using deprecated std::random_shuffle(); add tests
6302b74
@milkschen
reconcile update
18bc5fa
@milkschen
minor docstring improvements
dec8759
@milkschen
rename isec_frac -> isec_threshold
09e0c1f
@milkschen
allow setting bed_isec_threshold
b0b8b05
@milkschen
help message
9708406
@milkschen
add -B
f488702
@milkschen
update intersect()
6f4a6df
@milkschen milkschen marked this pull request as ready for review November 7, 2022 08:23
@milkschen milkschen merged commit 7f132b8 into main Nov 7, 2022
@milkschen milkschen deleted the dev branch November 7, 2022 08:24
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@milkschen