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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src/org/broadinstitute/sting	Updating HaplotypeCaller docs and expanding integration tests.	2012-07-23 10:05:42 -04:00
test/org/broadinstitute/sting/gatk/walkers	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