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Merge pull request #138 from broadinstitute/rp_hc_gga_alleles_rod_GSA-908 

Two changes to HC GGA mode to make it more like the UG.
This commit is contained in:
Mark DePristo 2013-04-01 08:28:23 -07:00
parent 7c83efc1b9 f65206e758
commit 791c386972
1 changed files with 3 additions and 6 deletions
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9
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -451,12 +451,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
public ActivityProfileState isActive( final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context ) { public ActivityProfileState isActive( final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context ) {
if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
for( final VariantContext vc : tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()) ) { final VariantContext vcFromAllelesRod = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, ref.getLocus(), false, logger, UG_engine.getUAC().alleles);
if( !allelesToGenotype.contains(vc) ) { if( vcFromAllelesRod != null ) {
allelesToGenotype.add(vc); // save for later for processing during the ActiveRegion's map call. Should be folded into a RefMetaDataTracker object allelesToGenotype.add(vcFromAllelesRod); // save for later for processing during the ActiveRegion's map call. Should be folded into a RefMetaDataTracker object
}
}
if( tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()).size() > 0 ) {
return new ActivityProfileState(ref.getLocus(), 1.0); return new ActivityProfileState(ref.getLocus(), 1.0);
} }
} }