From 7f0c63865362c938a00897a20f9d30b06a5d2ec9 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 1 Jun 2010 02:07:20 +0000
Subject: [PATCH] Fix for the indel cleaner: I forgot to "unclip" the cigar
 string (even though the clipped bases were removed) before using it as an
 alternate consensus in a particular instance.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3468 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java         | 8 ++++++--
 1 file changed, 6 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 3c881442a..2a54a7ab8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -719,6 +719,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             return null;
 
         // create the new consensus
+        ArrayList<CigarElement> elements = new ArrayList<CigarElement>(c.numCigarElements()-1);
         StringBuilder sb = new StringBuilder();
         for (int i = 0; i < indexOnRef; i++)
             sb.append((char)reference[i]);
@@ -732,8 +733,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             int elementLength = ce.getLength();
             switch( ce.getOperator() ) {
             case D:
-                indelCount++;
                 refIdx += elementLength;
+                indelCount++;
+                elements.add(ce);
                 break;
             case M:
                 altIdx += elementLength;
@@ -745,6 +747,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         sb.append((char)reference[refIdx+j]);
                 }
                 refIdx += elementLength;
+                elements.add(new CigarElement(elementLength, CigarOperator.M));
                 break;
             case I:
                 for (int j = 0; j < elementLength; j++) {
@@ -757,6 +760,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 }
                 altIdx += elementLength;
                 indelCount++;
+                elements.add(ce);
                 break;
             case S:
             default:
@@ -771,7 +775,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             sb.append((char)reference[i]);
         byte[] altConsensus =  StringUtil.stringToBytes(sb.toString()); // alternative consensus sequence we just built from the current read
 
-        return new Consensus(altConsensus, c, indexOnRef);
+        return new Consensus(altConsensus, new Cigar(elements), indexOnRef);
     }
 
     // create a Consensus from just the indel string that falls on the reference