From a89890891895a6095f77417f1ce27ecc57393ca1 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 17 Sep 2010 15:35:54 +0000
Subject: [PATCH] The output BAM file optional arguments of compression and
 whether to write an index are not outputs themselves.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4302 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../io/stubs/SAMFileWriterArgumentTypeDescriptor.java  | 10 +++++-----
 1 file 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 ffa6ac2b7..2570c142d 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
@@ -121,7 +121,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
      * @return Argument definition for the BAM file itself.  Will not be null.
      */
     private ArgumentDefinition createBAMArgumentDefinition(ArgumentSource source) {
-        Annotation annotation = this.getArgumentAnnotation(source);
+        Annotation annotation = getArgumentAnnotation(source);
         return new ArgumentDefinition( annotation,
                                        ArgumentIOType.getIOType(annotation),
                                        source.field.getType(),
@@ -144,8 +144,8 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
      * @return Argument definition for the BAM file itself.  Will not be null.
      */
     private ArgumentDefinition createBAMCompressionArgumentDefinition(ArgumentSource source) {
-        Annotation annotation = this.getArgumentAnnotation(source);
-        return new ArgumentDefinition( ArgumentIOType.getIOType(annotation),
+        Annotation annotation = getArgumentAnnotation(source);
+        return new ArgumentDefinition( ArgumentIOType.ARGUMENT,
                                        int.class,
                                        COMPRESSION_FULLNAME,
                                        COMPRESSION_SHORTNAME,
@@ -161,8 +161,8 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     }
 
     private ArgumentDefinition createWriteIndexArgumentDefinition(ArgumentSource source) {
-        Annotation annotation = this.getArgumentAnnotation(source);
-        return new ArgumentDefinition( ArgumentIOType.getIOType(annotation),
+        Annotation annotation = getArgumentAnnotation(source);
+        return new ArgumentDefinition( ArgumentIOType.ARGUMENT,
                                        boolean.class,
                                        CREATE_INDEX_FULLNAME,
                                        null,