Eric Banks ca9cd9b688 Minor fix for merging intervals which hadn't been necessary when only merging from the left to right. Added integration tests to cover the parallelization of RTC.		2011-10-06 22:38:44 -04:00
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R	Updated gsalib gsa.read.gatkreport to return all reports, even those beginning with '.'.	2011-10-05 18:30:40 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Minor fix for merging intervals which hadn't been necessary when only merging from the left to right. Added integration tests to cover the parallelization of RTC.	2011-10-06 22:38:44 -04:00
packages	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.	2011-09-27 14:33:57 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	GATK read group requirement iron hand	2011-10-06 08:40:35 -07:00
testdata	Oops, forgot the PED test file	2011-10-05 21:09:08 -07:00