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Merge pull request #530 from broadinstitute/vrr_gvcf_enabling_allele_trimming 

Activate reverse allele trimming in GVCF
This commit is contained in:
Valentin Ruano Rubio 2014-02-20 04:26:25 -05:00
parent 132e2429c8 463af7143f
commit a567a4d42c
2 changed files with 4 additions and 3 deletions
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3
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
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@ -229,9 +229,8 @@ public class GenotypingEngine {
VariantContext annotatedCall = annotationEngine.annotateContextForActiveRegion(tracker, stratifiedReadMap, call); VariantContext annotatedCall = annotationEngine.annotateContextForActiveRegion(tracker, stratifiedReadMap, call);
if( !emitReferenceConfidence && call.getAlleles().size() != mergedVC.getAlleles().size() ) { // some alleles were removed so reverseTrimming might be necessary! if( call.getAlleles().size() != mergedVC.getAlleles().size() )
annotatedCall = GATKVariantContextUtils.reverseTrimAlleles(annotatedCall); annotatedCall = GATKVariantContextUtils.reverseTrimAlleles(annotatedCall);
}
// maintain the set of all called haplotypes // maintain the set of all called haplotypes
for ( final Allele calledAllele : call.getAlleles() ) { for ( final Allele calledAllele : call.getAlleles() ) {

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
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@ -202,10 +202,12 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
// only re-genotype polymorphic sites // only re-genotype polymorphic sites
if ( result.isVariant() ) { if ( result.isVariant() ) {
final VariantContext regenotypedVC = genotypingEngine.calculateGenotypes(result); VariantContext regenotypedVC = genotypingEngine.calculateGenotypes(result);
if ( regenotypedVC == null ) if ( regenotypedVC == null )
return null; return null;
regenotypedVC = GATKVariantContextUtils.reverseTrimAlleles(regenotypedVC);
// we want to carry forward the attributes from the original VC but make sure to add the MLE-based annotations // we want to carry forward the attributes from the original VC but make sure to add the MLE-based annotations
final Map<String, Object> attrs = new HashMap<>(originalVC.getAttributes()); final Map<String, Object> attrs = new HashMap<>(originalVC.getAttributes());
attrs.put(VCFConstants.MLE_ALLELE_COUNT_KEY, regenotypedVC.getAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY)); attrs.put(VCFConstants.MLE_ALLELE_COUNT_KEY, regenotypedVC.getAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY));