3 Commits (3873dccb35eb904d2824c4ae8e7aad0c84c55635)

Author	SHA1	Message	Date
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