From 22f7fe0d52fddb8a354e4dba5f6bad42511c1265 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 31 Jan 2013 17:26:22 -0500
Subject: [PATCH] Expanded unit tests for AlignmentUtils

-- Added JIRA entries for the remaining capabilities to be fixed up and unit tested
---
 .../sting/gatk/walkers/annotator/ReadPosRankSumTest.java        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
index 95b31b732..ddca5e0b8 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
@@ -107,7 +107,7 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio
             final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true );
             if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED )
                 continue;
-            int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, false, 0, 0 );
+            int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, 0, 0 );
             final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read );
             if (readPos > numAlignedBases / 2)
                 readPos = numAlignedBases - (readPos + 1);