From 3a1b58ca6530afa3472247d5b4af77e77c602072 Mon Sep 17 00:00:00 2001 From: jmaguire Date: Fri, 19 Jun 2009 12:40:12 +0000 Subject: [PATCH] remove unused argument lodThreshold. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1057 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/playground/gatk/walkers/MultiSampleCaller.java | 1 - 1 file changed, 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java index 2838f361a..a08d1b3b3 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java @@ -25,7 +25,6 @@ public class MultiSampleCaller extends LocusWalker { @Argument(required=false, shortName="fractional_counts", doc="should we use fractional counts?") public boolean FRACTIONAL_COUNTS = false; @Argument(required=false, shortName="max_iterations", doc="Maximum number of iterations for EM") public int MAX_ITERATIONS = 10; - @Argument(fullName="lodThreshold", shortName="lod", required=false, doc="lod threshold for outputting individual genotypes") public Double lodThreshold = 0.0; @Argument(fullName="discovery_output", shortName="discovery_output", required=true, doc="file to write SNP discovery output to") public String DISCOVERY_OUTPUT; @Argument(fullName="individual_output", shortName="individual_output", required=true, doc="file to write individual SNP calls to") public String INDIVIDUAL_OUTPUT; @Argument(fullName="sample_name_regex", shortName="sample_name_regex", required=false, doc="sample_name_regex") public String SAMPLE_NAME_REGEX = null;