aaron 8b4d0412ca 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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1072 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-22 21:11:18 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	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
test/org/broadinstitute/sting	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