From 9c088fe3fee42a9a4b81e4b449bd4105cce53b9d Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 19 Oct 2012 12:41:24 -0400
Subject: [PATCH] Actually a better implementation of
 GATKSAMRecord.getSoftStart().  Last commit was all wrong.  Oops.

---
 .../broadinstitute/sting/utils/sam/GATKSAMRecord.java | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index 8c3d83874..1feb76517 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -388,9 +388,14 @@ public class GATKSAMRecord extends BAMRecord {
     public int getSoftStart() {
         if (softStart < 0) {
             softStart = getAlignmentStart();
-            final CigarElement firstCig = getCigar().getCigarElement(0);
-            if (firstCig.getOperator() == CigarOperator.HARD_CLIP)
-                softStart -= firstCig.getLength();
+            for (final CigarElement cig : getCigar().getCigarElements()) {
+                final CigarOperator op = cig.getOperator();
+
+                if (op == CigarOperator.SOFT_CLIP)
+                    softStart -= cig.getLength();
+                else if (op != CigarOperator.HARD_CLIP)
+                    break;
+            }
         }
         return softStart;
     }