From cd2bfb09ef30511f16ba7d5470f34b2de875893d Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 8 Sep 2010 13:59:09 +0000
Subject: [PATCH] Change for Tim: invalidate the MD tag (temporarily) if it
 exists in a read that gets realigned

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4228 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java              | 3 +++
 1 file changed, 3 insertions(+)

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 cf8712b3a..4b38d76eb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -592,6 +592,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                             read.setAttribute("NM", SequenceUtil.calculateSamNmTag(read, reference, (int)leftmostIndex-1));
                         if ( read.getAttribute(SAMTag.UQ.name()) != null )
                             read.setAttribute("UQ", SequenceUtil.sumQualitiesOfMismatches(read, reference, (int)leftmostIndex-1));
+                        // TODO -- this is only temporary until Tim adds code to recalculate this value
+                        if ( read.getAttribute(SAMTag.MD.name()) != null )
+                            read.setAttribute("MD", null);
                     }
                 }
             }