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

reads with no mate will be counted as valid reads
broadgsa · May 12, 2015 · 0b11ee4 · 0b11ee4
1 parent e142b5b
commit 0b11ee4
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/...ols-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java b/...ols-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java
@@ -245,7 +245,7 @@ protected String calculateLineForSite(final ReadBackedPileup pileup, final Strin
         for (final PileupElement base : pileup) {
             rawDepth++;
 
-            if (!base.getRead().getProperPairFlag()){
+            if (base.getRead().getReadPairedFlag() && (base.getRead().getMateUnmappedFlag() || !base.getRead().getProperPairFlag())){
                 improperPairsCount++;
                 continue;
             }