From 4a34c1862ee716c3dfff5e617377a45618781fd8 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 25 Oct 2011 15:22:28 -0400 Subject: [PATCH] misc cleanup. We now filter out haplotypes when it is obvious that the assembly has failed to find a parsimonious event rather than use haplotypes with large numbers of SNPs and small indels on them. --- .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 1 + 1 file changed, 1 insertion(+) 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 adb423145..9f0585d13 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 @@ -447,6 +447,7 @@ public class UnifiedGenotyperEngine { return new VariantCallContext(vcCall, confidentlyCalled(phredScaledConfidence, PofF)); } + // A barebones entry point to the exact model when there is no tracker or stratified contexts available -- only GLs public VariantCallContext calculateGenotypes(final VariantContext vc, final GenomeLoc loc, final GenotypeLikelihoodsCalculationModel.Model model) { // initialize the data for this thread if that hasn't been done yet