ebanks b75583a90b Adding debug statements for David to aid in testing the non-determinism problem. I wouldn't recommend running with --stats temporarily (or ever in fact, which is why it's @Hidden). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5907 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-31 19:53:59 +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	Adding debug statements for David to aid in testing the non-determinism problem. I wouldn't recommend running with --stats temporarily (or ever in fact, which is why it's @Hidden).	2011-05-31 19:53:59 +00:00
test	We now skip over all covering RODs in the BQSR as intended instead of just those which can be converted into a VariantContext. All the integration tests change because of subtleties in how certain dbsnp rod records are being converted into VCs. Added integration test which uses a bed file as the list of known polymorphic sites.	2011-05-27 16:32:17 +00:00