Mark DePristo 9cb3fe3a59 Vastly better way of doing on-demand genotyping loading ... -- With our GenotypesContext class we can naturally create a LazyGenotypesContext subclass that does the on-demand loading. -- This new class was replaced all of the old, complex functionality -- Better still, there were many cases were the genotypes were being loaded unnecessarily, resulting in efficiency. This was detected because some of the integration tests changed as the genotypes were no longer being parsing unnecessarily -- Misc. bug fixes throughout the system -- Bug fixes for PhaseByTransmission with new GenotypesContext		2011-11-20 08:23:09 -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	Vastly better way of doing on-demand genotyping loading	2011-11-20 08:23:09 -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jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	Should have been @BeforeMethod	2011-11-19 16:10:09 -05:00
BaseTest.java	merge master	2011-10-25 16:08:39 -04:00
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