Mark DePristo 73f9d1f217 GATK read group requirement iron hand ... -- The GATK will now throw a user exception if it opens a SAM/BAM file that doesn't have at least one RG defined -- LIBS again throws an error if the complete list of samples isn't provided -- Updating ExmpleCountLociPipeline test to use the well-formated versions of the exampleBAM and exampleFASTA files in testdata, instead of the old broken ones in validation_data. -- Convenience constructors for UserExceptions.MalformedBAM		2011-10-06 08:40:35 -07:00
..
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	GATK read group requirement iron hand	2011-10-06 08:40:35 -07:00
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