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SAMFileWriters specified as command-line arguments were sometimes incorrectly altering the default short name. Make sure short name is not specified if shortName is not specified but fullName is. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1807 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-10-09 19:16:46 +00:00
parent da084357db
commit d844d1c496
1 changed files with 17 additions and 2 deletions
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19
java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
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@ -38,6 +38,9 @@ import java.io.File;
* Insert a SAMFileWriterStub instead of a full-fledged concrete OutputStream implementations.
*/
public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
private static final String DEFAULT_ARGUMENT_FULLNAME = "outputBAM";
private static final String DEFAULT_ARGUMENT_SHORTNAME = "ob";
private static final String COMPRESSION_FULLNAME = "bam_compression";
private static final String COMPRESSION_SHORTNAME = "compress";
@ -92,8 +95,20 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
private ArgumentDefinition createBAMArgumentDefinition(ArgumentSource source) {
Argument description = this.getArgumentDescription(source);
String fullName = description.fullName().trim().length() > 0 ? description.fullName().trim() : "outputBAM";
String shortName = description.shortName().trim().length() > 0 ? description.shortName().trim() : "ob";
boolean isFullNameProvided = description.fullName().trim().length() > 0;
boolean isShortNameProvided = description.shortName().trim().length() > 0;
String fullName = isFullNameProvided ? description.fullName().trim() : DEFAULT_ARGUMENT_FULLNAME;
// If the short name is provided, use that. If the user hasn't provided any names at all, use
// the default. If somewhere in the middle, leave the short name blank.
String shortName;
if( isShortNameProvided )
shortName = description.shortName().trim();
else if( !isFullNameProvided )
shortName = DEFAULT_ARGUMENT_SHORTNAME;
else
shortName = null;
return new ArgumentDefinition( source,
fullName,