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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R	Fix a nasty bug in reading GATK reports with a single line	2012-09-10 20:14:13 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Fix GSA-515 Nanoscheduler GSA-573 -nt and -nct interact badly w.r.t. output	2012-09-20 18:45:16 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Update from dbsnp135 to dbsnp137.	2012-08-31 14:06:29 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00