From 16aa979e34be27ba1330489a7775a2ce4b61f1c4 Mon Sep 17 00:00:00 2001 From: asivache Date: Thu, 2 Apr 2009 22:23:46 +0000 Subject: [PATCH] make -A a true flag not an argument that asks for 'true/false' value! git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@278 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java index 0356b29e0..87920f1f5 100644 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java @@ -112,7 +112,7 @@ public class GenomeAnalysisTK extends CommandLineProgram { m_parser.addOptionalArg("downsample_to_fraction", "dfrac", "Fraction [0.0-1.0] of reads to downsample to", "DOWNSAMPLE_FRACTION"); m_parser.addOptionalArg("downsample_to_coverage", "dcov", "Coverage [integer] to downsample to", "DOWNSAMPLE_COVERAGE"); m_parser.addOptionalArg("intervals_file", "V", "File containing list of genomic intervals to operate on. line := ", "INTERVALS_FILE"); - m_parser.addOptionalArg("all_loci", "A", "Should we process all loci, not just those covered by reads", "WALK_ALL_LOCI"); + m_parser.addOptionalFlag("all_loci", "A", "Should we process all loci, not just those covered by reads", "WALK_ALL_LOCI"); m_parser.addOptionalArg("out", "o", "An output file presented to the walker. Will overwrite contents if file exists.", "outFileName" ); m_parser.addOptionalArg("err", "e", "An error output file presented to the walker. Will overwrite contents if file exists.", "errFileName" ); m_parser.addOptionalArg("outerr", "oe", "A joint file for 'normal' and error output presented to the walker. Will overwrite contents if file exists.", "outErrFileName");