Mark DePristo b5fa848255 Fix GSA-515 Nanoscheduler GSA-573 -nt and -nct interact badly w.r.t. output ... -- See https://jira.broadinstitute.org/browse/GSA-573 -- Uses InheritedThreadLocal storage so that children threads created by the NanoScheduler see the parent stubs in the main thread. -- Added explicit integration test that checks that -nt 1, 2 and -nct 1, 2 give the same results for GLM BOTH with the UG over 1 MB.		2012-09-20 18:45:16 -04:00
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net/sf	Fixing bug in fasta .fai generation: trim the contig names to the first whitespace if one appears. We now generate indexes identical to samtools.	2012-08-29 22:36:27 -04:00
org/broadinstitute/sting	Fix GSA-515 Nanoscheduler GSA-573 -nt and -nct interact badly w.r.t. output	2012-09-20 18:45:16 -04:00