From 2a937fa8d32ded1ef7f5a25197a5fa6b543c6bd1 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 17 Apr 2009 19:32:24 +0000
Subject: [PATCH] set SAM file header's sorting order to unsorted, hopefully it
 will help to speed things up

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@468 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/IndelInspector.java            | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java
index b41c06a39..48d1f9ddb 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java
@@ -49,6 +49,7 @@ public class IndelInspector extends ReadWalker<Integer, Integer> {
         }
 
         SAMFileHeader header = getToolkit().getSamReader().getFileHeader();
+        header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
         ptWriter = new PassThroughWriter(OUT1, header);
         if ( ! CONTROL_RUN ) pileBuilder = new PileBuilder(OUT2, header, ptWriter);