From 4a730adfc14677cbd0fac77af6c3a90afbfe8695 Mon Sep 17 00:00:00 2001 From: kcibul Date: Wed, 15 Jul 2009 20:44:02 +0000 Subject: [PATCH] committing latest changes before moving repositories git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1260 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/gatk/walkers/cancer/LocusReadPile.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/cancer/LocusReadPile.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/cancer/LocusReadPile.java index f641f0018..5cdeccdc9 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/cancer/LocusReadPile.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/cancer/LocusReadPile.java @@ -41,11 +41,12 @@ public class LocusReadPile { if (base == 'N' || base == 'n') { return; } - reads.add(read); - offsets.add(offset); + if (read.getMappingQuality() > 0) { + reads.add(read); + offsets.add(offset); - - likelihoods.add(refBase, base, qual); + likelihoods.add(refBase, base, qual); + } if (read.getMappingQuality() == 0 && !allowMapq0ForQualSum) { return; }