Khalid Shakir 677bea0abd Right aligning GATKReport numeric columns and updated MD5s in tests. ... PreQC parses file with spaces in sample names by using tabs only. PostQC allows passing the file names for the evals so that flanks can be evaled. BaseTest's network temp dir now adds the user name to the path so files aren't created in the root. HybridSelectionPipeline: - Updated to latest versions of reference data. - Refactored Picard parsing code replacing YAML.		2011-12-05 23:22:15 -05:00
..
alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Right aligning GATKReport numeric columns and updated MD5s in tests.	2011-12-05 23:22:15 -05:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00
utils	GenotypesContext now updates cached data for add, set, replace operations when possible	2011-11-22 08:40:48 -05:00
BaseTest.java	Right aligning GATKReport numeric columns and updated MD5s in tests.	2011-12-05 23:22:15 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00