From 7fbca7013e7b9da220396d9bcaec209efdf67cb7 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 6 Jun 2012 14:08:15 -0400 Subject: [PATCH] Don't add missing value binding from field to Genotype object in VCF3Codec --- .../org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java index 5bf8d4557..1489ac6b8 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java @@ -164,7 +164,7 @@ public class VCF3Codec extends AbstractVCFCodec { } else if (gtKey.equals(VCFConstants.GENOTYPE_FILTER_KEY)) { genotypeFilters = missing ? parseFilters(VCFConstants.MISSING_VALUE_v4) : parseFilters(getCachedString(GTValueArray[i])); } else if ( missing || GTValueArray[i].equals(VCFConstants.MISSING_GENOTYPE_QUALITY_v3) ) { - gtAttributes.put(gtKey, VCFConstants.MISSING_VALUE_v4); + //gtAttributes.put(gtKey, VCFConstants.MISSING_VALUE_v4); } else { gtAttributes.put(gtKey, new String(GTValueArray[i])); }