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solve bug - now work also when the reads does not have mate 

reads with no mate will be counted as valid reads
This commit is contained in:
Ami Levy-Moonshine 2015-03-31 15:08:25 -04:00
parent 7a75f4ae79
commit 536d550794
1 changed files with 1 additions and 1 deletions
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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) { for (final PileupElement base : pileup) {
rawDepth++; rawDepth++;
if (!base.getRead().getProperPairFlag()){ if (base.getRead().getReadPairedFlag() && (base.getRead().getMateUnmappedFlag() || !base.getRead().getProperPairFlag())){
improperPairsCount++; improperPairsCount++;
continue; continue;
} }