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Strictness args are presented as lowercase in the help, but only accepted if uppercase. Changed help to list the valid arguments in uppercase. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@376 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-13 00:50:19 +00:00
parent c51f51f255
commit 756e6c61d8
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -117,7 +117,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
m_parser.addOptionalArg("input_file", "I", "SAM or BAM file", "INPUT_FILE");
//m_parser.addRequiredArg("input_file", "I", "SAM or BAM file", "INPUT_FILE");
m_parser.addOptionalArg("maximum_reads", "M", "Maximum number of reads to process before exiting", "MAX_READS_ARG");
m_parser.addOptionalArg("validation_strictness", "S", "How strict should we be with validation (lenient|silent|strict)", "STRICTNESS_ARG");
m_parser.addOptionalArg("validation_strictness", "S", "How strict should we be with validation (LENIENT|SILENT|STRICT)", "STRICTNESS_ARG");
m_parser.addOptionalArg("reference_sequence", "R", "Reference sequence file", "REF_FILE_ARG");
m_parser.addOptionalArg("genome_region", "L", "Genome region to operation on: from chr:start-end", "REGION_STR");
m_parser.addRequiredArg("analysis_type", "T", "Type of analysis to run", "Analysis_Name");
@ -284,6 +284,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
catch( IllegalArgumentException ex ) {
strictness = ValidationStringency.STRICT;
}
logger.info("Strictness is " + strictness);
engine.setStrictness(strictness);