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committing latest changes before moving repositories 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1260 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-07-15 20:44:02 +00:00
parent 692b1e206f
commit 4a730adfc1
1 changed files with 5 additions and 4 deletions
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9
java/src/org/broadinstitute/sting/playground/gatk/walkers/cancer/LocusReadPile.java
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@ -41,11 +41,12 @@ public class LocusReadPile {
if (base == 'N' || base == 'n') { return; } if (base == 'N' || base == 'n') { return; }
reads.add(read); if (read.getMappingQuality() > 0) {
offsets.add(offset); reads.add(read);
offsets.add(offset);
likelihoods.add(refBase, base, qual);
likelihoods.add(refBase, base, qual); }
if (read.getMappingQuality() == 0 && !allowMapq0ForQualSum) { return; } if (read.getMappingQuality() == 0 && !allowMapq0ForQualSum) { return; }