gatk-3.8

Author	SHA1	Message	Date
hanna	ff798fe483	Reintroduce support for interval-based traversals. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@749 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-18 22:54:18 +00:00
hanna	2c4de7b5c5	Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along the pathway from command line to traversal engine. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@727 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-15 21:02:12 +00:00
hanna	9f5f6f9bc7	N-way parallelism. Works for small test cases. Untested for large test cases. -Needs more comprehensive unit testing. -Needs some basic refactoring. -Needs rethink of interface boundaries. -Needs to play more nicely in the /tmp sandbox. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@583 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-01 19:34:09 +00:00
hanna	3af66a462e	Make PrintLocusContextWalker less verbose. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@493 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-22 18:28:02 +00:00
hanna	e91a429c58	A class to print out as much context about the given locus site as is possible. Useful for testing traversal engines -- run old and new code across a given region and diff the output to make sure they have the same context. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@383 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-13 15:29:55 +00:00