Mark DePristo c0503283df Spelling fix requires md5 updates		2011-08-26 07:40:44 -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	Spelling fix requires md5 updates	2011-08-26 07:40:44 -04:00
jna	Avoid segfaults due to out of date and possibly abandonded LSF DRMAA implementation when use'ing LSF instead of .combined_LSF_SGE	2011-08-23 23:49:36 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	Fixing up and refactoring usage of indel categories. On a variant context, isInsertion() and isDeletion() are now removed because behavior before was wrong in case of multiallelic sites. Now, methods isSimpleInsertion() and isSimpleDeletion() will return true only if sites are biallelic. For multiallelic sites, isComplex() will return true in all cases.	2011-08-18 16:17:38 -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