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Fixing stray comments. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4102 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2010-08-24 20:19:39 +00:00
parent 85007ffa87
commit 7bbd67f3c4
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
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@ -78,11 +78,11 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
private int MAX_GAUSSIANS = 4;
@Argument(fullName="maxIterations", shortName="mI", doc="The maximum number of iterations to be performed when clustering. Clustering will normally end when convergence is detected.", required=false)
private int MAX_ITERATIONS = 200;
@Argument(fullName = "path_to_Rscript", shortName="Rscript", doc="The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
// private String PATH_TO_RSCRIPT = "Rscript";
// @Argument(fullName = "path_to_resources", shortName = "resources", doc="Path to resources folder holding the Sting R scripts.", required=false)
// private String PATH_TO_RESOURCES = "R/";
// @Argument(fullName="weightNovels", shortName="weightNovels", doc="The weight for novel variants during clustering", required=false)
// @Argument(fullName = "path_to_Rscript", shortName="Rscript", doc="The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
// private String PATH_TO_RSCRIPT = "Rscript";
// @Argument(fullName = "path_to_resources", shortName = "resources", doc="Path to resources folder holding the Sting R scripts.", required=false)
// private String PATH_TO_RESOURCES = "R/";
@Argument(fullName="weightNovels", shortName="weightNovels", doc="The weight for novel variants during clustering", required=false)
private double WEIGHT_NOVELS = 0.0;
@Argument(fullName="weightKnowns", shortName="weightKnowns", doc="The weight for MQ2+ known variants during clustering", required=false)
private double WEIGHT_KNOWNS = 0.0;