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Use @Output instead of @Argument. As a side note, Chris I'm ready for this nightmare to go away... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4835 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-12-14 17:13:15 +00:00
parent cf7d932a17
commit afd4655674
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
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@ -54,7 +54,7 @@ import net.sf.samtools.SAMReadGroupRecord;
public class BatchedCallsMerger extends LocusWalker<VariantContext, Integer> implements TreeReducible<Integer> {
@ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
@Argument(doc = "VCF file to which variants should be written", required = true)
@Output(doc = "VCF file to which variants should be written", required = true)
public VCFWriter writer = null;
@Argument(fullName="rod_list", shortName="rods", doc="A comma-separated string describing the rod names representing individual call batches", required=true)