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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commandline	Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"	2012-09-10 15:52:39 -04:00
gatk	Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table.	2012-09-20 14:14:34 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Fix GSA-515 Nanoscheduler GSA-573 -nt and -nct interact badly w.r.t. output	2012-09-20 18:45:16 -04:00
BaseTest.java	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Renaming -cnt to -nct for consistency	2012-09-05 21:13:19 -04:00