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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alignment	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
commandline	GATK Error messages now point to the new website instead of GetSatisfaction.	2012-07-20 17:27:11 -04:00
gatk	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
jna	Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.	2012-01-23 16:17:04 -05:00
queue	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
utils	Remove reference dependence in BCF2Codec	2012-07-25 08:56:38 -04:00