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

AD should be UNBOUNDED, actually 

-- Pass in # alt alleles as appropriate for getCount in VCF header line
This commit is contained in:
Mark DePristo 2012-05-16 20:33:46 -04:00
parent ac7460ef8c
commit b5bce8d3f9
2 changed files with 2 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
View File

@ -151,7 +151,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
return Arrays.asList( return Arrays.asList(
new VCFFormatHeaderLine( new VCFFormatHeaderLine(
getKeyNames().get(0), getKeyNames().get(0),
VCFHeaderLineCount.A, VCFHeaderLineCount.UNBOUNDED,
VCFHeaderLineType.Integer, VCFHeaderLineType.Integer,
"Allelic depths for the ref and alt alleles in the order listed")); "Allelic depths for the ref and alt alleles in the order listed"));
} }

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
View File

@ -221,7 +221,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
private final int getNGenotypeFieldValues(final String field, final VariantContext vc) { private final int getNGenotypeFieldValues(final String field, final VariantContext vc) {
final VCFCompoundHeaderLine metaData = VariantContext.getMetaDataForField(header, field); final VCFCompoundHeaderLine metaData = VariantContext.getMetaDataForField(header, field);
int nFields = metaData.getCount(vc.getNAlleles()); int nFields = metaData.getCount(vc.getNAlleles() - 1);
if ( nFields == -1 ) { // unbounded, need to look at values if ( nFields == -1 ) { // unbounded, need to look at values
return computeMaxSizeOfGenotypeFieldFromValues(field, vc); return computeMaxSizeOfGenotypeFieldFromValues(field, vc);
} else { } else {