From 6c6a324583592b390bd04456863b52a95f8b4a01 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Fri, 13 Jul 2012 15:24:46 -0400
Subject: [PATCH] Loosen a restriction on isOriginalRead()

* no longer needs to satisfy ReadAndIntervalOverlap.OVERLAP_CONTAINED
---
 .../gatk/walkers/compression/reducereads/ReduceReadsWalker.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
index 095149bae..1b11cbd4e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
@@ -663,7 +663,7 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
      * @return Returns true if the read is the original read that went through map().
      */
     private boolean isOriginalRead(LinkedList<GATKSAMRecord> list, GATKSAMRecord read) {
-        return isWholeGenome() || (list.getFirst().equals(read) && ReadUtils.getReadAndIntervalOverlapType(read, intervalList.first()) == ReadUtils.ReadAndIntervalOverlap.OVERLAP_CONTAINED);
+        return isWholeGenome() || list.getFirst().equals(read);
     }
 
     /**