Mark DePristo b08d63a6b8 Documentation and code cleanup for ClipReads, CallableLoci, and VariantsToTable ... -- Swapped -o [summary] and -ob [bam] for more standard -o [bam] and -os [summary] arguments. -- @Advanced arguments		2011-08-19 15:06:37 -04:00
..
alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Cleanup of codec locations. No more dbSNPHelper	2011-08-18 10:02:46 -04:00
gatk	Documentation and code cleanup for ClipReads, CallableLoci, and VariantsToTable	2011-08-19 15:06:37 -04:00
jna	Memory limits changed from Int to Double.	2011-07-21 22:57:18 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	Removed a public -> private dependency in our test suite.	2011-08-12 17:29:10 -04:00
BaseTest.java	Fixing syntax of BQSR and UG performance tests.	2011-08-11 17:04:09 -04:00
MD5DB.java	Go for global integrationtest path first, if possible.	2011-07-26 17:35:30 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -04:00