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Support for . values in qual field 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3752 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-07-09 01:47:02 +00:00
parent dd978dd525
commit 179067e3f4
1 changed files with 9 additions and 1 deletions
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10
java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
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@ -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;
}
}
/**