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gatk-3.8
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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
This commit is contained in:
kshakir 2010-09-17 15:35:54 +00:00
parent bc12055fcf
commit a898908918
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
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@ -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,