zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
View File

@ -121,7 +121,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
* @return Argument definition for the BAM file itself. Will not be null. * @return Argument definition for the BAM file itself. Will not be null.
*/ */
private ArgumentDefinition createBAMArgumentDefinition(ArgumentSource source) { private ArgumentDefinition createBAMArgumentDefinition(ArgumentSource source) {
Annotation annotation = this.getArgumentAnnotation(source); Annotation annotation = getArgumentAnnotation(source);
return new ArgumentDefinition( annotation, return new ArgumentDefinition( annotation,
ArgumentIOType.getIOType(annotation), ArgumentIOType.getIOType(annotation),
source.field.getType(), source.field.getType(),
@ -144,8 +144,8 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
* @return Argument definition for the BAM file itself. Will not be null. * @return Argument definition for the BAM file itself. Will not be null.
*/ */
private ArgumentDefinition createBAMCompressionArgumentDefinition(ArgumentSource source) { private ArgumentDefinition createBAMCompressionArgumentDefinition(ArgumentSource source) {
Annotation annotation = this.getArgumentAnnotation(source); Annotation annotation = getArgumentAnnotation(source);
return new ArgumentDefinition( ArgumentIOType.getIOType(annotation), return new ArgumentDefinition( ArgumentIOType.ARGUMENT,
int.class, int.class,
COMPRESSION_FULLNAME, COMPRESSION_FULLNAME,
COMPRESSION_SHORTNAME, COMPRESSION_SHORTNAME,
@ -161,8 +161,8 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
} }
private ArgumentDefinition createWriteIndexArgumentDefinition(ArgumentSource source) { private ArgumentDefinition createWriteIndexArgumentDefinition(ArgumentSource source) {
Annotation annotation = this.getArgumentAnnotation(source); Annotation annotation = getArgumentAnnotation(source);
return new ArgumentDefinition( ArgumentIOType.getIOType(annotation), return new ArgumentDefinition( ArgumentIOType.ARGUMENT,
boolean.class, boolean.class,
CREATE_INDEX_FULLNAME, CREATE_INDEX_FULLNAME,
null, null,