ebanks 4baeb5979f It turns out that Math.log10() can return 0, which leads to QUALs being set to -0, which is off-spec. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5415 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-10 03:08:56 +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	It turns out that Math.log10() can return 0, which leads to QUALs being set to -0, which is off-spec.	2011-03-10 03:08:56 +00:00
test	New attempt at the constrained movement version of the indel realigner (I've kept around the old writer for now). The new contract is that the realigner must ask permission before trying to clean an area; permission will be denied by the CM-Manager if it was required to flush its cache of reads because of too much depth within a distance of maxInsertSizeForMovingReadPairs. Added integration tests to cover different max cache sizes, including an expected exception when too small a value is chosen. The actual logic changes were fairly minor - much of this commit is really just some cleanup. I'd like to throw 1000G Phase I at it, but will respectfully wait for Ryan to hit his deadline before doing so.	2011-03-10 02:48:29 +00:00