depristo d7c0bcc223 Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information. ... All GenomeLoc[] are not ArrayList<GenomeLoc> for clarity and consistency Parsing now recursively merges contiguous elements chr1:1-10;chr1:11-20 => chr1:1-20 Added support for TraversingByLoci over all reference positions specified by the provided location array. System dynamically determines which traversal system to use. Pileup now marks, very clearly, reference positions without covered reads. Made changes around the codebase to deal with new GenomeLoc structure. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@218 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-28 20:37:27 +00:00
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executive	New type hierarchy for Traversals. There's a new package to hold them (traversals) and an easy system to create new ones. We are now one step closer to supporting the execution manager (a totally non-functional version is included here) that actually executes walkers in parallel using N threads.	2009-03-27 15:40:45 +00:00
iterators	Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information.	2009-03-28 20:37:27 +00:00
refdata	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
traversals	Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information.	2009-03-28 20:37:27 +00:00
walkers	Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information.	2009-03-28 20:37:27 +00:00
GenomeAnalysisTK.java	Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information.	2009-03-28 20:37:27 +00:00
LocusContext.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
WalkerManager.java	The traversal engine now passes the reduce result to OnTraversalDone() in the walker base class	2009-03-27 13:44:46 +00:00