From 8ff1a4b9299411b03734193cd6b73bbc763704d5 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 7 Jul 2010 19:49:36 +0000
Subject: [PATCH] Don't try to clean reads that fail the PF, in preparation for
 Ryan

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3730 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java | 1 +
 1 file changed, 1 insertion(+)

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 380365363..93921b6ad 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -295,6 +295,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     private boolean doNotTryToClean(SAMRecord read) {
         return read.getReadUnmappedFlag() ||
                 read.getNotPrimaryAlignmentFlag() ||
+                read.getReadFailsVendorQualityCheckFlag() ||
                 read.getMappingQuality() == 0 ||
                 read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ||
                 (!REALIGN_BADLY_MATED_READS && read.getReadPairedFlag() && !read.getMateUnmappedFlag() && read.getMateReferenceIndex() != read.getReferenceIndex());