From 32d502c122ba22f19742871808e8c59ea9ec567d Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 7 Apr 2011 23:44:25 +0000
Subject: [PATCH] Enable BAM OTF index writing by default.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5594 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java  | 6 +++---
 .../sting/utils/interval/IntervalIntegrationTest.java       | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
index 13d10961c..a08101f89 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
@@ -51,7 +51,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     public static final String SIMPLIFY_BAM_FULLNAME = "simplifyBAM";
     public static final String SIMPLIFY_BAM_SHORTNAME = SIMPLIFY_BAM_FULLNAME;
 
-    public static final String CREATE_INDEX_FULLNAME = "index_output_bam_on_the_fly";
+    public static final String CREATE_INDEX_FULLNAME = "disable_bam_indexing";
 
     /**
      * The engine into which output stubs should be fed.
@@ -117,7 +117,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
         if( compressionLevel != null )
             stub.setCompressionLevel(compressionLevel);
 
-        stub.setIndexOnTheFly(argumentIsPresent(createWriteIndexArgumentDefinition(source),matches));
+        stub.setIndexOnTheFly(!argumentIsPresent(createWriteIndexArgumentDefinition(source),matches));
         stub.setSimplifyBAM(argumentIsPresent(createSimplifyBAMArgumentDefinition(source),matches));
 
         // WARNING: Side effects required by engine!
@@ -176,7 +176,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
                                        boolean.class,
                                        CREATE_INDEX_FULLNAME,
                                        null,
-                                       "Create a BAM index on-the-fly while writing the resulting file.",
+                                       "Turn off on-the-fly creation of indices for output BAM files.",
                                        false,
                                        false,
                                        false,
diff --git a/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java b/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
index ecf8c475c..0f0a735f0 100644
--- a/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
@@ -69,7 +69,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -I " + validationDataLocation + "MV1994.bam" +
                         " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
                         " -L unmapped" +
-                        " -U --index_output_bam_on_the_fly",
+                        " -U",
                         0, // two output files
                         Collections.<String>emptyList());
 
@@ -89,7 +89,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -I " + validationDataLocation + "MV1994.bam" +
                         " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
                         " -XL unmapped" +
-                        " -U --index_output_bam_on_the_fly",
+                        " -U",
                         0, // two output files
                         Collections.<String>emptyList());