Merge branch 'main' into fix/format_multi_missing

molgenis · Jul 4, 2023 · f8cbb14 · f8cbb14
2 parents f9a6ef2 + 408fb0d
commit f8cbb14
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Showing 3 changed files with 11 additions and 6 deletions.
diff --git a/package.json b/package.json
@@ -1,9 +1,9 @@
 {
   "name": "@molgenis/vip-report-vcf",
-  "version": "1.3.5",
+  "version": "1.4.0",
   "description": "TypeScript VCF library with support for both reading and writing",
   "scripts": {
-    "preinstall": "curl --no-progress-meter --location https://github.com/molgenis/vip-utils/releases/download/v1.1.3/field_metadata.json --create-dirs --output src/metadata/field_metadata.json",
+    "preinstall": "curl --no-progress-meter --location https://github.com/molgenis/vip-utils/releases/download/v1.3.0/field_metadata.json --create-dirs --output src/metadata/field_metadata.json",
     "build": "tsc --build",
     "format": "prettier --write src/**/*.ts",
     "lint": "eslint src/**/*.ts",

diff --git a/src/VcfWriter.ts b/src/VcfWriter.ts
@@ -207,14 +207,16 @@ function writeString(value: string) {
 }
 
 function writeFormat(samples: RecordSample[]): string {
-  const keys = Object.keys(samples[0]);
+  const keys = Object.keys(samples[0]).filter((key) => key !== "VIAB");
   return keys.length > 0 ? keys.map(writeString).join(":") : MISSING;
 }
 
 function writeSample(formatFields: FormatMetadataContainer, sample: RecordSample): string {
   const vcf = [];
   for (const [key, value] of Object.entries(sample)) {
-    vcf.push(writeSampleValue(formatFields[key], value));
+    if (key !== "VIAB") {
+      vcf.push(writeSampleValue(formatFields[key], value));
+    }
   }
   return vcf.join(":");
 }

diff --git a/src/__tests__/VcfWriter.test.ts b/src/__tests__/VcfWriter.test.ts
@@ -35,9 +35,10 @@ test("parse and write vcf: Samples filtered", () => {
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
 ##contig=<ID=1,length=249250621,assembly=b37>
 #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1\tSAMPLE2
-1\t1\t.\tA\tG\t.\t.\t.\tGT:GQ:HQ\t0/1:.:4,5\t1/1
+1\t1\t.\tA\tG\t.\t.\t.\tGT:AD:GQ:HQ\t0/1:20,80:.:4,5\t1/1
 `;
   expect(writeVcf(parseVcf(vcfSamples), { samples: ["SAMPLE1", "SAMPLE2"] })).toBe(expectedVcfSamples);
 });
@@ -47,6 +48,7 @@ test("parse and write vcf: Samples none", () => {
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
 ##contig=<ID=1,length=249250621,assembly=b37>
 #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO
 1\t1\t.\tA\tG\t.\t.\t.
@@ -136,9 +138,10 @@ const vcfSamples = `##fileformat=VCFv4.2
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
 ##contig=<ID=1,length=249250621,assembly=b37>
 #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE0\tSAMPLE1\tSAMPLE2
-1\t1\t.\tA\tG\t.\t.\t.\tGT:GQ:HQ\t0|1:1:2,3\t0/1:.:4,5\t1/1
+1\t1\t.\tA\tG\t.\t.\t.\tGT:AD:GQ:HQ\t0|1:1,50:1:2,3\t0/1:20,80:.:4,5\t1/1
 `;
 
 const vcfSamplesMissingValues = `##fileformat=VCFv4.2