From a12933a26d70c0812f155a4ab15cff319fb5c0ec Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 15 Jan 2010 20:58:48 +0000
Subject: [PATCH] Bug fixed: now the length of an insertion is determined
 correctly. Thought I committed this...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2599 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/iterators/LocusIteratorByState.java              | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
index fc946c9a1..8c432f371 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
@@ -191,7 +191,7 @@ public class LocusIteratorByState extends LocusIterator {
                         // past the insertion right after that
                         if ( eventDelayedFlag > 1 ) throw new StingException("Adjacent I/D events in read "+read.getReadName());
                         insertedBases = Arrays.copyOfRange(read.getReadBases(),readOffset+1,readOffset+1+curElement.getLength());
-                        eventLength = cigarElementCounter ;
+                        eventLength = curElement.getLength() ;
                         eventStart = readOffset;
                         eventDelayedFlag = 2; // insertion causes re-entry into stepForwardOnGenome, so we set the delay to 2
 //                        System.out.println("Inserted "+(new String (insertedBases)) +" after "+readOffset);