From 536d5507943745fd73c5279c2b05c95ff5960b75 Mon Sep 17 00:00:00 2001
From: Ami Levy-Moonshine <ami@broadinstitute.org>
Date: Tue, 31 Mar 2015 15:08:25 -0400
Subject: [PATCH] solve bug - now work also when the reads does not have mate
 reads with no mate will be counted as valid reads

---
 .../gatk/tools/walkers/rnaseq/ASEReadCounter.java               | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java
index 9812d1001..a5622d570 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java
@@ -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;
             }