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Bug fix: if there are samples in the VCF but all of them are no-calls, we still need to emit GT for the FORMAT field to be on spec. Note that this is a holdover from 3.3 writing but can't easily be fixed there. Fortunately, that code is all going away soon... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3754 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-07-09 14:08:25 +00:00
parent ea8fd506bf
commit abaec13e38
1 changed files with 3 additions and 0 deletions
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java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
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@ -344,6 +344,9 @@ public class VCFWriter {
if ( allowedGenotypeAttributeKeys == null || allowedGenotypeAttributeKeys.contains(key) ) if ( allowedGenotypeAttributeKeys == null || allowedGenotypeAttributeKeys.contains(key) )
vcfGenotypeAttributeKeys.add(key); vcfGenotypeAttributeKeys.add(key);
} }
} else if ( header.hasGenotypingData() ) {
// this needs to be done in case all samples are no-calls
vcfGenotypeAttributeKeys.add(VCFGenotypeRecord.GENOTYPE_KEY);
} }
String genotypeFormatString = Utils.join(GENOTYPE_FIELD_SEPARATOR, vcfGenotypeAttributeKeys); String genotypeFormatString = Utils.join(GENOTYPE_FIELD_SEPARATOR, vcfGenotypeAttributeKeys);