From 179067e3f42b47b18591aeeb5bece7cd02fee6c4 Mon Sep 17 00:00:00 2001 From: depristo Date: Fri, 9 Jul 2010 01:47:02 +0000 Subject: [PATCH] Support for . values in qual field git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3752 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/refdata/features/vcf4/VCF4Codec.java | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java index 1d12f39d1..90afdd594 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java @@ -269,7 +269,15 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec { */ private static Double parseQual(String qualString) { // todo -- remove double once we deal with annoying VCFs from 1KG - return qualString.equals("-1") || qualString.equals("-1.0") ? VariantContext.NO_NEG_LOG_10PERROR : Double.valueOf(qualString) / 10; + if ( qualString.equals(".") ) + return VariantContext.NO_NEG_LOG_10PERROR; + else { + double q = Double.valueOf(qualString); + if ( q == -1 ) + return VariantContext.NO_NEG_LOG_10PERROR; + else + return Double.valueOf(qualString) / 10; + } } /**