Mauricio Carneiro e89ff063fc GATKSAMRecord refactor ... The GATK engine will now provide a GATKSAMRecord to all tools which incorporates the functionality used by the GATK to the bam file (ReadGroups, Reduced Reads, ...). * No tools should create SAMRecord anymore, use GATKSAMRecord instead *		2011-11-03 15:43:26 -04:00
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R	Compacting pdfs when running under R 2.13+.	2011-10-27 14:51:56 -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	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
packages	No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.	2011-10-27 14:17:07 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Bug fix to avoid infinite loop in GATKScatterFunction	2011-11-02 16:20:42 -04:00
testdata	Oops, forgot the PED test file	2011-10-05 21:09:08 -07:00