From fc55dcec3c0fe2ed72fcd924d9065202d56013fe Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 1 May 2012 16:02:36 -0400 Subject: [PATCH] Unfortunately the reverse trimming of alleles still doesn't work with mixed records in some corner cases. Turning it off for now. --- .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index caa3a6b6b..a1d02b27f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -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() ) {