zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Don't add missing value binding from field to Genotype object in VCF3Codec

This commit is contained in:
Mark DePristo 2012-06-06 14:08:15 -04:00
parent cfd1e50068
commit 7fbca7013e
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
View File

@ -164,7 +164,7 @@ public class VCF3Codec extends AbstractVCFCodec {
} else if (gtKey.equals(VCFConstants.GENOTYPE_FILTER_KEY)) { } else if (gtKey.equals(VCFConstants.GENOTYPE_FILTER_KEY)) {
genotypeFilters = missing ? parseFilters(VCFConstants.MISSING_VALUE_v4) : parseFilters(getCachedString(GTValueArray[i])); genotypeFilters = missing ? parseFilters(VCFConstants.MISSING_VALUE_v4) : parseFilters(getCachedString(GTValueArray[i]));
} else if ( missing || GTValueArray[i].equals(VCFConstants.MISSING_GENOTYPE_QUALITY_v3) ) { } 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 { } else {
gtAttributes.put(gtKey, new String(GTValueArray[i])); gtAttributes.put(gtKey, new String(GTValueArray[i]));
} }