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Now supports multiple records in allele at sites that genotype as reference 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5796 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-05-12 17:36:27 +00:00
parent 66c8fa5c48
commit db1f9af679
2 changed files with 20 additions and 14 deletions
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30
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
View File

@ -54,6 +54,23 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES; useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
} }
public static VariantContext getSNPVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, boolean requireSNP, Logger logger) {
VariantContext vc = null;
// search for usable record
for( final VariantContext vc_input : tracker.getVariantContexts(ref, "alleles", null, ref.getLocus(), true, false) ) {
if ( vc_input != null && ! vc_input.isFiltered() && (! requireSNP || vc_input.isSNP() )) {
if ( vc == null ) {
vc = vc_input;
} else {
logger.warn("Multiple valid VCF records detected at site " + ref.getLocus() + ", only considering alleles from first record only");
}
}
}
return vc;
}
public Allele getLikelihoods(RefMetaDataTracker tracker, public Allele getLikelihoods(RefMetaDataTracker tracker,
ReferenceContext ref, ReferenceContext ref,
Map<String, AlignmentContext> contexts, Map<String, AlignmentContext> contexts,
@ -73,18 +90,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
if ( alternateAlleleToUse != null ) { if ( alternateAlleleToUse != null ) {
bestAlternateAllele = alternateAlleleToUse.getBases()[0]; bestAlternateAllele = alternateAlleleToUse.getBases()[0];
} else if ( useAlleleFromVCF ) { } else if ( useAlleleFromVCF ) {
VariantContext vc = null; VariantContext vc = getSNPVCFromAllelesRod(tracker, ref, true, logger);
// search for usable record
for( final VariantContext vc_input : tracker.getVariantContexts(ref, "alleles", null, ref.getLocus(), true, false) ) {
if ( vc_input != null && ! vc_input.isFiltered() && vc_input.isSNP() ) {
if ( vc == null ) {
vc = vc_input;
} else {
logger.warn("Multiple valid VCF records detected at site " + ref.getLocus() + ", only considering alleles from first record only");
}
}
}
// ignore places where we don't have a variant // ignore places where we don't have a variant
if ( vc == null ) if ( vc == null )

4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -198,8 +198,8 @@ public class UnifiedGenotyperEngine {
private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, AlignmentContext rawContext) { private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, AlignmentContext rawContext) {
VariantContext vc; VariantContext vc;
if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true); VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger);
if ( vcInput == null || vcInput.isFiltered() ) if ( vcInput == null )
return null; return null;
vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles()); vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles());
} else { } else {