From 78d5ac9bc2db5229a58943e885e00488a1202967 Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 10 Dec 2009 04:07:47 +0000 Subject: [PATCH] Don't check het count when there are multiple Genotypes per Variation. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2304 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/varianteval/VariantCounter.java | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java index 6736f2350..f121e1ffd 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java @@ -31,9 +31,11 @@ public class VariantCounter extends BasicVariantAnalysis implements GenotypeAnal public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) { nSNPs += eval == null ? 0 : 1; - if ( this.getMaster().evalContainsGenotypes && eval != null ) { - Genotype genotype = ((VariantBackedByGenotype)eval).getCalledGenotype(); - if ( eval.isSNP() && eval.isBiallelic() && genotype.isHet() ) { + // TODO -- break the het check out to a different module used only for single samples + + if ( this.getMaster().evalContainsGenotypes && eval != null && eval.isBiallelic() && eval.isSNP() ) { + List genotypes = ((VariantBackedByGenotype)eval).getGenotypes(); + if ( genotypes.size() == 1 && genotypes.get(0).isHet() ) { nHets++; } }