From 95b29f608b29c63d1157dc25ae192d9f611a84d0 Mon Sep 17 00:00:00 2001 From: kiran Date: Fri, 14 May 2010 21:42:53 +0000 Subject: [PATCH] Specify default values. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3364 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/diagnostics/ComputeConfusionMatrix.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java index 458537dc7..d7eecd620 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java @@ -45,13 +45,13 @@ import java.util.Hashtable; */ @Reference(window=@Window(start=-5,stop=5)) public class ComputeConfusionMatrix extends LocusWalker { - @Argument(fullName="minimumDepth", shortName="minDepth", doc="Require locus pileup to have specified minimum depth", required=false) + @Argument(fullName="minimumDepth", shortName="minDepth", doc="Require locus pileup to have specified minimum depth (default: 10)", required=false) public Integer MIN_DEPTH = 10; - @Argument(fullName="maximumDepth", shortName="maxDepth", doc="Require locus pileup to have specified maximum depth", required=false) + @Argument(fullName="maximumDepth", shortName="maxDepth", doc="Require locus pileup to have specified maximum depth (default: 100)", required=false) public Integer MAX_DEPTH = 100; - @Argument(fullName="contextWindowSize", shortName="window", doc="Size of context window", required=false) + @Argument(fullName="contextWindowSize", shortName="window", doc="Size of context window (default: 0)", required=false) public Integer WINDOW_SIZE = 0; private Hashtable confusionCounts = new Hashtable();