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Fix for when running with EMIT_ALL_SITES but not GENOTYPE_GIVEN_ALLELES. Still want to emit a site even when over the deletion fraction for example. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5617 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-04-12 20:07:06 +00:00
parent 488622041d
commit 30a19a00fe
2 changed files with 14 additions and 11 deletions
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23
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -151,9 +151,10 @@ public class UnifiedGenotyperEngine {
}
Map<String, AlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
if ( stratifiedContexts == null )
return (UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES ? null : generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext));
if ( stratifiedContexts == null ) {
return (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext) : null);
}
VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model);
if ( vc == null )
@ -459,7 +460,7 @@ public class UnifiedGenotyperEngine {
ReadBackedExtendedEventPileup pileup = rawPileup.getMappingFilteredPileup(UAC.MIN_MAPPING_QUALTY_SCORE);
// don't call when there is no coverage
if ( pileup.size() == 0 && UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES )
if ( pileup.size() == 0 && !(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) )
return null;
// stratify the AlignmentContext and cut by sample
@ -473,12 +474,14 @@ public class UnifiedGenotyperEngine {
// stratify the AlignmentContext and cut by sample
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup(), UAC.ASSUME_SINGLE_SAMPLE);
int numDeletions = 0;
for( final PileupElement p : rawContext.getBasePileup() ) {
if( p.isDeletion() ) { numDeletions++; }
}
if( ((double) numDeletions) / ((double) rawContext.getBasePileup().size()) > UAC.MAX_DELETION_FRACTION ) {
return null;
if( !(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) ) {
int numDeletions = 0;
for( final PileupElement p : rawContext.getBasePileup() ) {
if( p.isDeletion() ) { numDeletions++; }
}
if( ((double) numDeletions) / ((double) rawContext.getBasePileup().size()) > UAC.MAX_DELETION_FRACTION ) {
return null;
}
}
}

2
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -153,7 +153,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-sites_only", "63b76c4d26edf8cbb5bd91dafc81fee1" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "5bf0268945d953377ea3a811b20ff1bc" );
e.put( "--output_mode EMIT_ALL_SITES", "a1730ea5ae5e1aa57d85d9d2372facc8" );
e.put( "--output_mode EMIT_ALL_SITES", "78eeff5b2277877954e4985934077d3f" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(