Add the PS FORMAT VCF standard header field (#1200)

Add a standardized VCF headerline for the PS field.
samtools · Oct 24, 2018 · 334800e · 334800e
1 parent bbc674f
commit 334800e
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/src/main/java/htsjdk/variant/vcf/VCFStandardHeaderLines.java b/src/main/java/htsjdk/variant/vcf/VCFStandardHeaderLines.java
@@ -158,6 +158,7 @@ private static void registerStandard(final VCFFormatHeaderLine line) {
         registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY,        VCFHeaderLineCount.G,         VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
         registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS, VCFHeaderLineCount.R,         VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed"));
         registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY,    VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String,  "Genotype-level filter"));
+        registerStandard(new VCFFormatHeaderLine(VCFConstants.PHASE_SET_KEY,          1,                            VCFHeaderLineType.Integer, "Phasing set (typically the position of the first variant in the set)"));
         registerStandard(new VCFFormatHeaderLine(VCFConstants.PHASE_QUALITY_KEY,      1,                            VCFHeaderLineType.Float,   "Read-backed phasing quality"));
 
         // INFO lines