From 3ee0311fdb998105e2e1ff0c9e7b7a7c23d940d5 Mon Sep 17 00:00:00 2001
From: seru71 <pawel.sztromwasser@gmail.com>
Date: Tue, 10 Feb 2015 14:11:05 +0100
Subject: [PATCH] corrected logical expression in MateSameStrandFilter

Signed-off-by: David Roazen <droazen@broadinstitute.org>
---
 .../gatk/engine/filters/MateSameStrandFilter.java               | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java
index 0818f8fa0..c6a79e1a3 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java
@@ -37,6 +37,6 @@ public class MateSameStrandFilter extends ReadFilter {
 
     public boolean filterOut(SAMRecord read) {
         return (! read.getReadPairedFlag() ) || read.getMateUnmappedFlag() || read.getDuplicateReadFlag() ||
-                read.getReadFailsVendorQualityCheckFlag() || read.getMateNegativeStrandFlag() != read.getReadNegativeStrandFlag();
+                read.getReadFailsVendorQualityCheckFlag() || (read.getMateNegativeStrandFlag() == read.getReadNegativeStrandFlag());
     }
 }