Mark DePristo 31f4e5b52e Stop unlimited runtimes in DiffEngine when you have lots of differences ... -- Added a new parameter to control the maximum number of pairwise differences to generate, which previously could expand to a very large number when there were lots of differences among genotypes, resulting in a n^2 algorithm running with n > 1,000,000		2012-05-27 11:17:13 -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	Yet More missing md5's	2012-05-25 17:21:47 -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	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	Stop unlimited runtimes in DiffEngine when you have lots of differences	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	Oops, don't enable shadow BCF tests	2012-05-24 13:31:13 -04:00