From da11efa1a2c18e61e595b98fc124483efae843f7 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 3 Sep 2010 14:10:44 +0000
Subject: [PATCH] Automatically write BAM file indices for coordinate-sorted
 BAMs.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4209 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/io/storage/SAMFileWriterStorage.java           | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
index b8dd1553d..dea36e112 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
@@ -50,6 +50,10 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
     public SAMFileWriterStorage( SAMFileWriterStub stub, File file ) {
         this.file = file;
         SAMFileWriterFactory factory = new SAMFileWriterFactory();
+        // Enable automatic index creation for pre-sorted BAMs.
+        if (stub.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate))
+            factory.setCreateIndex(true);
+        // Adjust max records in RAM.
         if(stub.getMaxRecordsInRam() != null)
             factory.setMaxRecordsInRam(stub.getMaxRecordsInRam());