From b806a9cf68403af97740ca4d3a8e45d7a07e8b63 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 20 Mar 2009 20:38:24 +0000
Subject: [PATCH] Updated for new version of samtools, which returns a sequence
 dictionary rather than a simple list of sequences.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@121 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../src/org/broadinstitute/sting/indels/IndelInspector.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java b/playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java
index fdf50c55e..7b16b94bb 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java
+++ b/playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java
@@ -250,7 +250,7 @@ public class IndelInspector extends CommandLineProgram {
             setDefaultContigOrdering();
             return;
         }
-        List<SAMSequenceRecord> seqs = h.getSequences();
+        List<SAMSequenceRecord> seqs = h.getSequenceDictionary().getSequences();
         if ( seqs == null ) {
             System.out.println("No reference sequence records found in SAM file header, " +
                                "falling back to default contig ordering");