Eric Banks a5721a8846 Context covariate optimizations were not suited for multiple threads, so I removed them (since that ended up being much, much easier than trying to make the covariates thread local). Added -nt 2 layer to BQSR integration tests to confirm that it now works with multiple threads.		2012-07-25 13:38:07 -04:00
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bqsr	Context covariate optimizations were not suited for multiple threads, so I removed them (since that ended up being much, much easier than trying to make the covariates thread local). Added -nt 2 layer to BQSR integration tests to confirm that it now works with multiple threads.	2012-07-25 13:38:07 -04:00
compression/reducereads	Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests.	2012-07-10 02:04:26 -04:00
genotyper	FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing	2012-07-18 16:07:47 -04:00
haplotypecaller	Updating HaplotypeCaller docs and expanding integration tests.	2012-07-23 10:05:42 -04:00