From 756e6c61d8c55739f550a5fca8593590874d4862 Mon Sep 17 00:00:00 2001 From: kiran Date: Mon, 13 Apr 2009 00:50:19 +0000 Subject: [PATCH] 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 --- java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java index 9419c0241..52273a3d3 100644 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java @@ -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);