hanna 9b182e3063 Prep for documenting command-line arguments: delete some arguments that don't make sense any more given ... the state of the traversals and GATK input requirements: all_loci (replaced by walker annotation), max OTF sorts (bam files must be sorted and indexed), threaded io (replaced by data sharding framework). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1144 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-01 18:23:35 +00:00
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org/broadinstitute/sting	Prep for documenting command-line arguments: delete some arguments that don't make sense any more given	2009-07-01 18:23:35 +00:00