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a couple of quick name changes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@976 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-06-10 20:02:52 +00:00
parent 72a81f8f25
commit 026f68fb41
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java
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@ -43,7 +43,7 @@ import java.util.ArrayList;
public class SomaticCoverageTool extends CommandLineExecutable { public class SomaticCoverageTool extends CommandLineExecutable {
// the two sam/bam files, one for cancer, one for normal // the two sam/bam files, one for cancer, one for normal
@Argument(fullName = "bam_files", shortName = "I", doc = "The bam files, one for the tumor one for the normal", required = true) @Argument(fullName = "bam_file", shortName = "I", doc = "The bam files, one for the tumor one for the normal", required = true)
public List<File> samFiles = new ArrayList<File>(); public List<File> samFiles = new ArrayList<File>();
@ -70,7 +70,7 @@ public class SomaticCoverageTool extends CommandLineExecutable {
/** override any arguments we see fit. */ /** override any arguments we see fit. */
protected void overrideArguments() { protected void overrideArguments() {
this.argCollection = GATKArgumentCollection.unmarshal("SomaticCoverage.xml"); this.argCollection = GATKArgumentCollection.unmarshal("SomaticCoverage.xml");
this.argCollection.intervals = "CancerIntervals.interval"; this.argCollection.intervals = "CancerIntervals.list";
this.argCollection.samFiles = samFiles; this.argCollection.samFiles = samFiles;
} }
} }