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Merge pull request #979 from broadinstitute/ami-fixASE-bug 

solve bug - now work also when the reads does not have mate
This commit is contained in:
Geraldine Van der Auwera 2015-05-14 21:09:52 -04:00
parent dee66b06fa 536d550794
commit 8b20523f5e
1 changed files with 1 additions and 1 deletions
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2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java
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@ -245,7 +245,7 @@ public class ASEReadCounter extends LocusWalker<String, Integer> {
for (final PileupElement base : pileup) {
rawDepth++;
if (!base.getRead().getProperPairFlag()){
if (base.getRead().getReadPairedFlag() && (base.getRead().getMateUnmappedFlag() || !base.getRead().getProperPairFlag())){
improperPairsCount++;
continue;
}