From fe9f12863182bad1cb51c0dc61e13945b5d119e4 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 12 Oct 2010 19:21:33 +0000
Subject: [PATCH] Better fix for earlier bug.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4484 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java             | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index c30e6e112..9c971b10f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -924,9 +924,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             // for reads that end in an insertion
             if ( myPosOnAlt + aRead.getReadLength() < endOfFirstBlock + indelCE.getLength() ) {
                 int partialInsertionLength = myPosOnAlt + aRead.getReadLength() - endOfFirstBlock;
-                // if we also started inside the insertion, then we need to modify the length by 1 base
+                // if we also started inside the insertion, then we need to modify the length
                 if ( !sawAlignmentStart )
-                    partialInsertionLength--;
+                    partialInsertionLength = aRead.getReadLength();
                 readCigar.add(new CigarElement(partialInsertionLength, CigarOperator.I));
                 aRead.setCigar(readCigar);
                 return true;