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Fix for invalid format error when outputting BAM files. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1438 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-08-19 19:42:39 +00:00
parent 4cf9110468
commit 21091b9839
2 changed files with 2 additions and 5 deletions
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4
java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java
View File

@ -352,8 +352,8 @@ class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
COMPRESSION_SHORTNAME, COMPRESSION_SHORTNAME,
"Compression level to use for writing BAM files", "Compression level to use for writing BAM files",
false, false,
"", null,
"" ); null );
return Arrays.asList( writerDefinition, compressionDefinition ); return Arrays.asList( writerDefinition, compressionDefinition );
} }

3
java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
View File

@ -258,9 +258,6 @@ public class ParsingEngine {
if( argumentMatches.size() == 0 ) if( argumentMatches.size() == 0 )
return; return;
if( argumentMatches.size() > 1 )
throw new StingException("Too many values matched argument: " + source.field.getName());
if( source.clazz.isAssignableFrom(target.getClass()) ) { if( source.clazz.isAssignableFrom(target.getClass()) ) {
Object value = source.parse( source, target, argumentMatches.toArray(new ArgumentMatch[0]) ); Object value = source.parse( source, target, argumentMatches.toArray(new ArgumentMatch[0]) );
if( clp == null || !clp.intercept(source, target, value) ) if( clp == null || !clp.intercept(source, target, value) )