aaron 04e5b28f6d updates for VCF; we can no longer cache genotypes or alleles in a static array, this is bad for sharred memory parallel runs. One instance per codec was better for performance than using ThreadLocal code. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4063 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-19 19:34:44 +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	updates for VCF; we can no longer cache genotypes or alleles in a static array, this is bad for sharred memory parallel runs. One instance per codec was better for performance than using ThreadLocal code.	2010-08-19 19:34:44 +00:00
test	Fix for running the cleaner at the lane-level for known indels only: instead of relying on the reads to get the reference sequence, we now use an IndexedFastaSequenceFile in all cases and pad the reference with bases on either end. This allows us to deal with cases in which we are trying to clean just a single deletion-containing read with tiny LOD (so the read needs to be pushed off the seen reference; @Reference doesn't yet work for Read Walkers) and has the added benefit of allowing us now to get much larger known indels that aren't completely covered with reads.	2010-08-19 11:31:13 +00:00