From b7a67da775908e693f81022461823d22b912b3f1 Mon Sep 17 00:00:00 2001
From: jmaguire <jmaguire@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 2 Apr 2009 21:38:00 +0000
Subject: [PATCH] Expose the underlying SAM reader to the walkers.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@270 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java   | 3 +++
 .../broadinstitute/sting/gatk/traversals/TraversalEngine.java  | 2 ++
 2 files changed, 5 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index 0b73700fe..0356b29e0 100644
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 import edu.mit.broad.picard.reference.ReferenceSequenceFile;
 import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
+import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMFileReader.ValidationStringency;
 import net.sf.samtools.SAMSequenceRecord;
 import net.sf.samtools.util.RuntimeIOException;
@@ -395,4 +396,6 @@ public class GenomeAnalysisTK extends CommandLineProgram {
                     contig.getName(), refFile.getDistanceBetweenContigs("chr1", contig.getName())));
         }
     }
+
+    public SAMFileReader getSamReader() { return this.engine.getSamReader(); }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index 4fca25941..48e4293d0 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -538,4 +538,6 @@ public abstract class TraversalEngine {
                 logger.warn(msg);
         }
     }
+
+    public SAMFileReader getSamReader() { return this.samReader; }
 }