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Matt pointed out that some long names were capitalized and some were not, and that's just plain uncool; to which I agreed. Now that's fixed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@152 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-03-23 15:01:32 +00:00
parent 08ca2ce89b
commit 27353af216
1 changed files with 3 additions and 3 deletions
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6
core/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -66,9 +66,9 @@ public class GenomeAnalysisTK extends CommandLineProgram {
m_parser.addOptionalArg("genome_region", "L", "Genome region to operation on: from chr:start-end", "REGION_STR");
m_parser.addRequiredlArg("analysis_type", "T", "Type of analysis to run", "Analysis_Name");
m_parser.addOptionalArg("DBSNP", "D", "DBSNP file", "DBSNP_FILE");
m_parser.addOptionalFlag("Threaded_IO", "P", "If set, enables threaded I/O operations", "ENABLED_THREADED_IO");
m_parser.addOptionalFlag("Unsafe", "U", "If set, enables unsafe operations, nothing will be checked at runtime.", "UNSAFE");
m_parser.addOptionalFlag("Sort_on_the_fly", "F", "If set, enables on fly sorting of reads file.", "ENABLED_SORT_ON_FLY");
m_parser.addOptionalFlag("threaded_IO", "P", "If set, enables threaded I/O operations", "ENABLED_THREADED_IO");
m_parser.addOptionalFlag("unsafe", "U", "If set, enables unsafe operations, nothing will be checked at runtime.", "UNSAFE");
m_parser.addOptionalFlag("sort_on_the_fly", "F", "If set, enables on fly sorting of reads file.", "ENABLED_SORT_ON_FLY");
m_parser.addOptionalArg("intervals_file", "V", "File containing list of genomic intervals to operate on. line := <contig> <start> <end>", "INTERVALS_FILE");
}