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Fix to allow haplotype caller to call indels after UG engine entry points were unified. Adding Haplotype Caller integration test

This commit is contained in:
Ryan Poplin 2011-12-13 17:19:40 -05:00
parent 7a386b45a5
commit 7fa1ab1bae
1 changed files with 4 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -371,8 +371,11 @@ public class UnifiedGenotyperEngine {
builder.log10PError(phredScaledConfidence/-10.0); builder.log10PError(phredScaledConfidence/-10.0);
if ( ! passesCallThreshold(phredScaledConfidence) ) if ( ! passesCallThreshold(phredScaledConfidence) )
builder.filters(filter); builder.filters(filter);
if ( !limitedContext ) if ( limitedContext ) {
builder.referenceBaseForIndel(vc.getReferenceBaseForIndel());
} else {
builder.referenceBaseForIndel(refContext.getBase()); builder.referenceBaseForIndel(refContext.getBase());
}
// create the genotypes // create the genotypes
GenotypesContext genotypes = assignGenotypes(vc, altAllelesToUse); GenotypesContext genotypes = assignGenotypes(vc, altAllelesToUse);