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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
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asivache 2009-04-02 22:23:46 +00:00
parent decf45664a
commit 16aa979e34
1 changed files with 1 additions and 1 deletions
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java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -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 := <contig> <start> <end>", "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");