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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.

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Ryan Poplin 2011-10-25 15:22:28 -04:00
parent 13702939ac
commit 4a34c1862e
1 changed files with 1 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -447,6 +447,7 @@ public class UnifiedGenotyperEngine {
return new VariantCallContext(vcCall, confidentlyCalled(phredScaledConfidence, PofF)); 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) { 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 // initialize the data for this thread if that hasn't been done yet