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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TraversalEngine.java	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
TraversalStatistics.java	Fixes for including duplicate reads in the locus traversal; now checks that the ref arg is provided when needed	2009-04-17 01:27:36 +00:00
TraverseDuplicates.java	Changed the duplicate traversal over to the new style of traversal and plumbed into the genome analysis engine. Also added a CountDuplicates walker, to validate the engine.	2009-06-22 21:11:18 +00:00
TraverseLoci.java	Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.	2009-06-11 18:13:22 +00:00
TraverseLocusWindows.java	TraverseByLocusWindow -- asstd bug fixes.	2009-06-25 22:51:38 +00:00
TraverseReads.java	Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.	2009-06-22 14:39:41 +00:00
package.html	Package level documentation -- helps new users get acclimated to the codebase more quickly.	2009-06-17 16:27:48 +00:00