From 69652e08c64762b2e114cbb8ffafd6efb8e89488 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 12 Oct 2010 14:46:21 +0000
Subject: [PATCH] Bug fix for reads that completely fall within an insertion:
 the I cigar string element was 1 base too long.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4482 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java           | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

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 f497d8dd1..c30e6e112 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -923,7 +923,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         if ( indelCE.getOperator() == CigarOperator.I ) {
             // for reads that end in an insertion
             if ( myPosOnAlt + aRead.getReadLength() < endOfFirstBlock + indelCE.getLength() ) {
-                readCigar.add(new CigarElement(myPosOnAlt + aRead.getReadLength() - endOfFirstBlock, CigarOperator.I));
+                int partialInsertionLength = myPosOnAlt + aRead.getReadLength() - endOfFirstBlock;
+                // if we also started inside the insertion, then we need to modify the length by 1 base
+                if ( !sawAlignmentStart )
+                    partialInsertionLength--;
+                readCigar.add(new CigarElement(partialInsertionLength, CigarOperator.I));
                 aRead.setCigar(readCigar);
                 return true;
             }