Merge d7f4321 into 39ca07c

hammerlab · May 7, 2021 · 7883c62 · 7883c62
2 parents 39ca07c + d7f4321
commit 7883c62
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Showing 3 changed files with 39 additions and 1 deletion.
diff --git a/src/main/data/vcf.js b/src/main/data/vcf.js
@@ -153,7 +153,7 @@ class ImmediateVcfFile {
     var contigMap = {};
     contigs.forEach(contig => {
       if (contig.slice(0, 3) == 'chr') {
-        contigMap[contig.slice(4)] = contig;
+        contigMap[contig.slice(3)] = contig;
       } else {
         contigMap['chr' + contig] = contig;
       }

diff --git a/src/test/data/vcf-test.js b/src/test/data/vcf-test.js
@@ -80,6 +80,16 @@ describe('VCF', function() {
     });
   });
 
+  it('should remove chr', function(): any {
+    var vcf = new VcfFile(new RemoteFile('/test-data/snv-chr-prefix.vcf'));
+    var range = new ContigInterval('20', 63799, 69094);
+    return vcf.getFeaturesInRange(range).then(features => {
+      expect(features).to.have.length(6);
+      expect(features[0].variant.contig).to.equal('chr20'); // not 20
+      expect(features[5].variant.contig).to.equal('chr20');
+    });
+  });
+
   it('should handle unsorted VCFs', function(): any {
     var vcf = new VcfFile(new RemoteFile('/test-data/sort-bug.vcf'));
     var chr1 = new ContigInterval('chr1', 1, 1234567890);

diff --git a/test-data/snv-chr-prefix.vcf b/test-data/snv-chr-prefix.vcf
@@ -0,0 +1,28 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
+##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
+##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
+##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
+##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
+##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
+##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
+##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
+chr20	61795	.	G	T	.	PASS	DP=81;SS=1;SSC=2;GPV=4.6768E-16;SPV=5.4057E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:44:22:22:50%:16,6,9,13	0/1:.:37:18:19:51.35%:10,8,10,9
+chr20	62731	.	C	A	.	PASS	DP=68;SS=1;SSC=1;GPV=1.4855E-11;SPV=7.5053E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:32:17:15:46.88%:9,8,9,6	0/1:.:36:21:15:41.67%:8,13,8,7
+chr20	63799	.	C	T	.	PASS	DP=72;SS=1;SSC=7;GPV=3.6893E-16;SPV=1.8005E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:39:19:19:50%:8,11,11,8	0/1:.:33:12:21:63.64%:5,7,8,13
+chr20	65288	.	G	T	.	PASS	DP=35;SS=1;SSC=0;GPV=7.8434E-5;SPV=8.2705E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:21:13:8:38.1%:4,9,0,8	0/1:.:14:10:4:28.57%:2,8,0,4
+chr20	65900	.	G	A	.	PASS	DP=53;SS=1;SSC=0;GPV=1.5943E-31;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:26:0:26:100%:0,0,12,14	1/1:.:27:0:27:100%:0,0,15,12
+chr20	66370	.	G	A	.	PASS	DP=66;SS=1;SSC=0;GPV=2.6498E-39;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:32:0:32:100%:0,0,11,21	1/1:.:34:0:34:100%:0,0,15,19
+chr20	68749	.	T	C	.	PASS	DP=64;SS=1;SSC=0;GPV=4.1752E-38;SPV=1E0	GT:GQ:DP:RD:AD:FREQ:DP4	1/1:.:23:0:23:100%:0,0,7,16	1/1:.:41:0:41:100%:0,0,21,20
+chr20	69094	.	G	A	.	PASS	DP=25;SS=1;SSC=8;GPV=4.2836E-5;SPV=1.5657E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:12:8:4:33.33%:5,3,4,0	0/1:.:13:5:8:61.54%:3,2,6,2
+chr20	69408	.	C	T	.	PASS	DP=53;SS=1;SSC=0;GPV=8.7266E-12;SPV=9.8064E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:27:9:18:66.67%:5,4,9,9	0/1:.:26:15:11:42.31%:6,9,4,7
+chr20	75254	.	C	A	.	PASS	DP=74;SS=1;SSC=9;GPV=7.9203E-12;SPV=1.1567E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/1:.:34:22:11:33.33%:13,9,5,6	0/1:.:40:20:20:50%:5,15,14,6