From d70483c50a74e6d4ddf81e08eae6eac3a8dd8040 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 31 Dec 2010 04:42:54 +0000
Subject: [PATCH] Automatically filter out reads with consecutive indel
 operators in the CIGAR string

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4914 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/RealignerTargetCreator.java   | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index 6264fa1c7..6b0d855b8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -28,13 +28,13 @@ package org.broadinstitute.sting.gatk.walkers.indels;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.filters.BadCigarFilter;
 import org.broadinstitute.sting.gatk.filters.Platform454Filter;
 import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
@@ -48,9 +48,9 @@ import java.util.ArrayList;
 import java.io.PrintStream;
 
 /**
- * Emits intervals for the Local Indel Realigner to target for cleaning.  Ignores 454 and MQ0 reads.
+ * Emits intervals for the Local Indel Realigner to target for cleaning.  Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string.
  */
-@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
+@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, BadCigarFilter.class})
 @Reference(window=@Window(start=-1,stop=50))
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @By(DataSource.REFERENCE)