4 Commits (de9f1f575f2a322effc938dce7c9f339496976df)

Author	SHA1	Message	Date
depristo	dfc36c1e95	Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3445 348d0f76-0448-11de-a6fe-93d51630548a	2010-05-26 22:12:25 +00:00
hanna	02f48b6457	Fix bug that's been in the GATK for a very long time: update nReads (as well ... as nRecords), so that INFO logging doesn't say 'skipped 0 of 0 reads'. While I'm in there, update TraversalStatistics to store longs. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2959 348d0f76-0448-11de-a6fe-93d51630548a	2010-03-08 22:44:54 +00:00
depristo	dbf2344cef	Fixes for including duplicate reads in the locus traversal; now checks that the ref arg is provided when needed ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@459 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-17 01:27:36 +00:00
hanna	8a1207e4db	Bringing up scaffolding for integration of locus traversals by reference with Aaron's data source code. ... Reverts to original TraverseByLociByReference behavior unless a special combination of command-line flags are used. Lightly tested at best, and major flaws include: - MicroManager is not doing MicroScheduling right now; it's driving the traversals. - New database-ish data providers imply by their interface that they're stateless, but they're highly stateful. - Using static objects to circumvent encapsulation. - Code duplication is rampant. - Plus more! git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@346 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-09 20:28:17 +00:00