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Unfortunately the reverse trimming of alleles still doesn't work with mixed records in some corner cases. Turning it off for now.

This commit is contained in:
Ryan Poplin 2012-05-01 16:02:36 -04:00
parent 2187d71bb2
commit fc55dcec3c
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -419,7 +419,7 @@ public class UnifiedGenotyperEngine {
// if we are subsetting alleles (either because there were too many or because some were not polymorphic)
// then we may need to trim the alleles (because the original VariantContext may have had to pad at the end).
if ( myAlleles.size() != vc.getAlleles().size() )
if ( myAlleles.size() != vc.getAlleles().size() && !limitedContext ) // TODO - this function doesn't work with mixed records or records that started as mixed and then became non-mixed
vcCall = VariantContextUtils.reverseTrimAlleles(vcCall);
if ( annotationEngine != null && !limitedContext && rawContext.hasBasePileup() ) {