Mark DePristo 06b02e1b9b Update MD5s to reflect new limited output of DiffObjectsWalkers ... -- Also updated GQ change in VCFIntegrationTest		2012-05-27 11:20:47 -04:00
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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	Update MD5s to reflect new limited output of DiffObjectsWalkers	2012-05-27 11:20:47 -04:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	Update MD5s to reflect new limited output of DiffObjectsWalkers	2012-05-27 11:20:47 -04:00
BaseTest.java	Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests	2012-05-27 11:17:17 -04:00
MD5DB.java	Even more conservative limit on number of differences to summarize at 1000	2012-05-27 11:17:13 -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	Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests	2012-05-27 11:17:17 -04:00