Add lowercase test file

GMOD · Jun 17, 2022 · 2126af2 · 2126af2
1 parent 6b31038
commit 2126af2
Show file tree

Hide file tree

Showing 4 changed files with 117 additions and 1 deletion.
diff --git a/products/jbrowse-cli/src/commands/add-track.ts b/products/jbrowse-cli/src/commands/add-track.ts
@@ -664,6 +664,7 @@ export default class AddTrack extends JBrowseCommand {
       IndexedFastaAdapter: 'ReferenceSequenceTrack',
       TwoBitAdapter: 'ReferenceSequenceTrack',
       VcfTabixAdapter: 'VariantTrack',
+      VcfAdapter: 'VariantTrack',
       HicAdapter: 'HicTrack',
       PAFAdapter: 'SyntenyTrack',
     }

diff --git a/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap b/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap
@@ -3033,6 +3033,36 @@ Object {
       "trackId": "spliced",
       "type": "AlignmentsTrack",
     },
+    Object {
+      "adapter": Object {
+        "type": "VcfAdapter",
+        "vcfLocation": Object {
+          "internetAccountId": undefined,
+          "internetAccountPreAuthorization": undefined,
+          "locationType": "UriLocation",
+          "uri": "volvox.filtered.lowercase.vcf",
+        },
+      },
+      "assemblyNames": Array [
+        "volvox",
+      ],
+      "category": Array [
+        "Integration test",
+      ],
+      "displays": Array [
+        Object {
+          "displayId": "volvox.filtered.lowercase-LinearBasicDisplay",
+          "type": "LinearBasicDisplay",
+        },
+        Object {
+          "displayId": "volvox.filtered.lowercase-LinearArcDisplay",
+          "type": "LinearArcDisplay",
+        },
+      ],
+      "name": "volvox.filtered.lowercase",
+      "trackId": "volvox.filtered.lowercase",
+      "type": "FeatureTrack",
+    },
   ],
 }
 `;
diff --git a/test_data/volvox/trix/volvox_meta.json b/test_data/volvox/trix/volvox_meta.json
@@ -1,5 +1,5 @@
 {
-  "dateCreated": "2022-04-14T23:41:01.028Z",
+  "dateCreated": "2022-06-17T10:57:18.370Z",
   "tracks": [
     {
       "trackId": "volvox_sv_test",
@@ -145,6 +145,18 @@
           "indexType": "TBI"
         }
       }
+    },
+    {
+      "trackId": "volvox.filtered.lowercase",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfAdapter",
+        "vcfLocation": {
+          "uri": "volvox.filtered.lowercase.vcf",
+          "locationType": "UriLocation"
+        }
+      }
     }
   ],
   "assemblyNames": ["volvox"]

diff --git a/test_data/volvox/volvox.filtered.lowercase.vcf b/test_data/volvox/volvox.filtered.lowercase.vcf
@@ -0,0 +1,73 @@
+##fileformat=VCFv4.1
+##samtoolsVersion=0.1.18 (r982:295)
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
+##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
+##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
+##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
+##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
+##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##contig=<ID=ctga,length=248956422,assembly=GRCh38.d1.vd1>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_data/raw/volvox/volvox-sorted.bam
+ctga	277	.	T	C	10.4	.	DP=3;VDB=0.0186;AF1=1;AC1=2;DP4=0,0,3,0;MQ=37;FQ=-36	GT:PL:GQ	1/1:42,9,0:13
+ctga	1694	.	T	C	107	.	DP=23;VDB=0.0308;AF1=1;AC1=2;DP4=0,1,8,14;MQ=37;FQ=-73;PV4=1,1,0.42,1	GT:PL:GQ	1/1:140,46,0:89
+ctga	2644	.	T	G	44	.	DP=22;VDB=0.0253;AF1=0.5;AC1=1;DP4=6,5,3,8;MQ=37;FQ=45.3;PV4=0.39,1,1,1	GT:PL:GQ	0/1:74,0,77:75
+ctga	3213	.	T	A	124	.	DP=19;VDB=0.0384;AF1=1;AC1=2;DP4=0,0,8,11;MQ=36;FQ=-84	GT:PL:GQ	1/1:157,57,0:99
+ctga	3858	.	ctt	ct	160	.	INDEL;DP=15;VDB=0.0384;AF1=1;AC1=2;DP4=0,0,5,6;MQ=37;FQ=-67.5	GT:PL:GQ	1/1:201,33,0:63
+ctga	5496	.	C	G	6.98	.	DP=18;VDB=0.0011;AF1=0.4999;AC1=1;DP4=5,7,4,2;MQ=37;FQ=9.53;PV4=0.62,1,1,1	GT:PL:GQ	0/1:36,0,92:37
+ctga	8471	.	G	T	124	.	DP=21;VDB=0.0355;AF1=1;AC1=2;DP4=0,0,11,10;MQ=37;FQ=-90	GT:PL:GQ	1/1:157,63,0:99
+ctga	9603	.	A	T	126	.	DP=21;VDB=0.0356;AF1=1;AC1=2;DP4=0,0,10,11;MQ=36;FQ=-90	GT:PL:GQ	1/1:159,63,0:99
+ctga	10423	.	T	A	25	.	DP=19;VDB=0.0404;AF1=0.5;AC1=1;DP4=3,7,3,6;MQ=37;FQ=28;PV4=1,1,1,0.27	GT:PL:GQ	0/1:55,0,73:58
+ctga	13202	.	G	T	40	.	DP=22;VDB=0.0399;AF1=0.5;AC1=1;DP4=4,8,5,5;MQ=37;FQ=42.8;PV4=0.67,1,1,1	GT:PL:GQ	0/1:70,0,84:73
+ctga	14247	.	ac	aCc	61.5	.	INDEL;DP=22;VDB=0.0404;AF1=0.5;AC1=1;DP4=3,4,6,0;MQ=37;FQ=62.4;PV4=0.07,1,1,1	GT:PL:GQ	0/1:99,0,101:99
+ctga	14481	.	G	A	42	.	DP=21;VDB=0.0394;AF1=0.5;AC1=1;DP4=4,6,5,6;MQ=37;FQ=42;PV4=1,1,1,0.12	GT:PL:GQ	0/1:72,0,72:72
+ctga	15078	.	T	A	96	.	DP=12;VDB=0.0404;AF1=1;AC1=2;DP4=0,0,4,8;MQ=37;FQ=-63	GT:PL:GQ	1/1:129,36,0:69
+ctga	15163	.	gcc	gCcc	213	.	INDEL;DP=20;VDB=0.0404;AF1=1;AC1=2;DP4=0,0,10,7;MQ=37;FQ=-85.5	GT:PL:GQ	1/1:254,51,0:99
+ctga	15418	.	A	G	64	.	DP=19;VDB=0.0253;AF1=0.5003;AC1=1;DP4=5,1,5,8;MQ=35;FQ=4.13;PV4=0.14,0.26,0.11,1	GT:PL:GQ	0/1:94,0,29:32
+ctga	17042	.	C	T	119	.	DP=22;VDB=0.0394;AF1=1;AC1=2;DP4=0,0,13,9;MQ=37;FQ=-93	GT:PL:GQ	1/1:152,66,0:99
+ctga	18948	.	A	G	57	.	DP=23;VDB=0.0308;AF1=0.5;AC1=1;DP4=6,4,4,9;MQ=37;FQ=39;PV4=0.22,1,0.2,1	GT:PL:GQ	0/1:87,0,66:69
+ctga	19882	.	acg	a	98.5	.	INDEL;DP=22;VDB=0.0374;AF1=0.5;AC1=1;DP4=4,6,3,5;MQ=37;FQ=101;PV4=1,0.049,1,1	GT:PL:GQ	0/1:136,0,202:99
+ctga	20675	.	T	C	40	.	DP=18;VDB=0.0401;AF1=0.5;AC1=1;DP4=5,3,4,6;MQ=36;FQ=31.7;PV4=0.64,1,0.19,0.15	GT:PL:GQ	0/1:70,0,59:62
+ctga	21485	.	C	T,A	118	.	DP=20;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,8,12;MQ=36;FQ=-84	GT:PL:GQ	1/1:151,57,0,150,42,147:99
+ctga	22326	.	C	T	107	.	DP=14;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,6,8;MQ=36;FQ=-69	GT:PL:GQ	1/1:140,42,0:81
+ctga	23636	.	A	C	58	.	DP=19;VDB=0.0320;AF1=0.5;AC1=1;DP4=2,5,5,7;MQ=37;FQ=18.1;PV4=0.66,0.23,1,0.037	GT:PL:GQ	0/1:88,0,45:48
+ctga	23959	.	A	G	118	.	DP=19;VDB=0.0374;AF1=1;AC1=2;DP4=0,0,7,11;MQ=36;FQ=-81	GT:PL:GQ	1/1:151,54,0:99
+ctga	24978	.	C	G	127	.	DP=22;VDB=0.0355;AF1=1;AC1=2;DP4=0,0,11,11;MQ=35;FQ=-93	GT:PL:GQ	1/1:160,66,0:99
+ctga	25558	.	A	C	104	.	DP=27;VDB=0.0371;AF1=1;AC1=2;DP4=0,0,18,7;MQ=36;FQ=-102	GT:PL:GQ	1/1:137,75,0:99
+ctga	26079	.	C	A	29	.	DP=18;VDB=0.0339;AF1=0.5;AC1=1;DP4=6,4,4,4;MQ=36;FQ=31.9;PV4=1,0.14,0.44,0.13	GT:PL:GQ	0/1:59,0,76:62
+ctga	28463	.	T	A	27	.	DP=20;VDB=0.0399;AF1=0.5;AC1=1;DP4=5,6,4,5;MQ=36;FQ=30;PV4=1,1,1,1	GT:PL:GQ	0/1:57,0,82:60
+ctga	28719	.	T	G	39	.	DP=18;VDB=0.0333;AF1=0.5;AC1=1;DP4=6,3,5,4;MQ=37;FQ=36.6;PV4=1,1,1,1	GT:PL:GQ	0/1:69,0,65:67
+ctga	29032	.	G	T	103	.	DP=19;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,13,6;MQ=37;FQ=-84	GT:PL:GQ	1/1:136,57,0:99
+ctga	29848	.	C	T	91	.	DP=11;VDB=0.0333;AF1=1;AC1=2;DP4=0,0,5,6;MQ=36;FQ=-60	GT:PL:GQ	1/1:124,33,0:63
+ctga	34015	.	T	A	85	.	DP=10;VDB=0.0339;AF1=1;AC1=2;DP4=0,0,4,6;MQ=37;FQ=-57	GT:PL:GQ	1/1:118,30,0:57
+ctga	35771	.	T	A	99	.	DP=16;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,3,13;MQ=36;FQ=-75	GT:PL:GQ	1/1:132,48,0:93
+ctga	38156	.	C	G	16.1	.	DP=12;VDB=0.0168;AF1=0.5;AC1=1;DP4=3,2,3,2;MQ=37;FQ=16.1;PV4=1,1,1,0.43	GT:PL:GQ	0/1:46,0,46:46
+ctga	39952	.	C	T	124	.	DP=21;VDB=0.0404;AF1=1;AC1=2;DP4=0,0,11,10;MQ=33;FQ=-90	GT:PL:GQ	1/1:157,63,0:99
+ctga	39966	.	T	C	11.3	.	DP=27;VDB=0.0299;AF1=0.5;AC1=1;DP4=11,5,2,7;MQ=34;FQ=14.2;PV4=0.041,1,0.01,1	GT:PL:GQ	0/1:41,0,88:43
+ctga	39983	.	A	T	127	.	DP=24;VDB=0.0355;AF1=1;AC1=2;DP4=0,0,13,11;MQ=34;FQ=-99	GT:PL:GQ	1/1:160,72,0:99
+ctga	41826	.	T	C	110	.	DP=18;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,11,7;MQ=36;FQ=-81	GT:PL:GQ	1/1:143,54,0:99
+ctga	42608	.	G	T	31	.	DP=24;VDB=0.0404;AF1=0.5;AC1=1;DP4=10,4,3,7;MQ=36;FQ=34;PV4=0.095,0.12,0.044,1	GT:PL:GQ	0/1:61,0,82:64
+ctga	43007	.	T	A	36	.	DP=19;VDB=0.0355;AF1=0.5;AC1=1;DP4=3,5,9,2;MQ=36;FQ=30.4;PV4=0.074,1,0.11,1	GT:PL:GQ	0/1:66,0,58:60
+ctga	43354	.	A	C	35	.	DP=20;VDB=0.0147;AF1=0.5;AC1=1;DP4=5,6,5,4;MQ=37;FQ=37.9;PV4=1,1,1,0.39	GT:PL:GQ	0/1:65,0,82:68
+ctga	45666	.	G	T,A	91	.	DP=16;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,10,6;MQ=36;FQ=-72	GT:PL:GQ	1/1:124,45,0,122,31,119:87
+ctga	46994	.	T	A	40	.	DP=24;VDB=0.0308;AF1=0.5;AC1=1;DP4=6,7,7,4;MQ=37;FQ=43;PV4=0.44,1,1,0.49	GT:PL:GQ	0/1:70,0,89:73
+ctga	47847	.	C	A,T	126	.	DP=23;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,9,14;MQ=36;FQ=-93	GT:PL:GQ	1/1:159,66,0,158,51,155:99
+ctga	48199	.	A	T	22	.	DP=17;VDB=0.0320;AF1=0.5;AC1=1;DP4=2,8,4,3;MQ=36;FQ=25;PV4=0.16,1,0.12,0.0062	GT:PL:GQ	0/1:52,0,71:55
+ctga	49288	.	G	A	106	.	DP=23;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,16,7;MQ=35;FQ=-96	GT:PL:GQ	1/1:139,69,0:99