Mark DePristo 7280cdf937 Bugfixes and testdata cleanup ... -- Cut down the size of a few large files in public/testdata that were only used in part -- Refactor vcf Filename => shadow BCF filename to BCF2Utils. Fix bug in WalkerTest due to the way this was handled previously		2012-05-24 13:26:05 -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	Bugfixes and testdata cleanup	2012-05-24 13:26:05 -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	Bugfixes and testdata cleanup	2012-05-24 13:26:05 -04:00
BaseTest.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
MD5DB.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -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 testdata cleanup	2012-05-24 13:26:05 -04:00