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GENOTYPE_GIVEN_ALLELES now respects the filter status of the incoming alleles file. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5466 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-03-18 02:59:28 +00:00
parent 6281c1db6f
commit 9b8d41160b
3 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
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@ -291,7 +291,7 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo
if (getAlleleListFromVCF) {
for( final VariantContext vc_input : tracker.getVariantContexts(ref, "alleles", null, ref.getLocus(), false, false) ) {
if( vc_input != null && vc_input.isIndel() && ref.getLocus().getStart() == vc_input.getStart()) {
if( vc_input != null && ! vc_input.isFiltered() && vc_input.isIndel() && ref.getLocus().getStart() == vc_input.getStart()) {
vc = vc_input;
break;
}

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -71,7 +71,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
bestAlternateAllele = alternateAlleleToUse.getBases()[0];
} else if ( useAlleleFromVCF ) {
final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true);
if ( vcInput == null )
if ( vcInput == null || vcInput.isFiltered() )
return null;
if ( !vcInput.isSNP() ) {
logger.info("Record at position " + ref.getLocus() + " is not a SNP; skipping...");

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -208,7 +208,7 @@ public class UnifiedGenotyperEngine {
VariantContext vc;
if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true);
if ( vcInput == null )
if ( vcInput == null || vcInput.isFiltered() )
return null;
vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles());
} else {