From 026f68fb4181d901cb5abf014a7ce1181b4d574b Mon Sep 17 00:00:00 2001 From: aaron Date: Wed, 10 Jun 2009 20:02:52 +0000 Subject: [PATCH] a couple of quick name changes git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@976 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/playground/somaticcoverage/SomaticCoverageTool.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java b/java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java index 9d49b10b2..b4c868299 100644 --- a/java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java +++ b/java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java @@ -43,7 +43,7 @@ import java.util.ArrayList; public class SomaticCoverageTool extends CommandLineExecutable { // 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 samFiles = new ArrayList(); @@ -70,7 +70,7 @@ public class SomaticCoverageTool extends CommandLineExecutable { /** override any arguments we see fit. */ protected void overrideArguments() { this.argCollection = GATKArgumentCollection.unmarshal("SomaticCoverage.xml"); - this.argCollection.intervals = "CancerIntervals.interval"; + this.argCollection.intervals = "CancerIntervals.list"; this.argCollection.samFiles = samFiles; } }