Eric Banks 1e90d602a4 Optimization: cache up front the PL index to the pair of alleles it represents for all possible numbers of alternate alleles.		2011-12-14 13:38:20 -05:00
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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Optimization: cache up front the PL index to the pair of alleles it represents for all possible numbers of alternate alleles.	2011-12-14 13:38:20 -05:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00
utils	Turning off test that breaks read clipper	2011-12-09 11:53:12 -05:00
BaseTest.java	Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-12-07 09:03:17 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00