Mauricio Carneiro 663184ee9d Added test mode to PPP ... * in test mode, no @PG tags are output to the final bam file * updated pipeline test to use -test mode. * MD5s updated accordingly		2011-12-12 18:29:06 -05:00
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R	scales=free shows variance within analysis better	2011-12-07 14:09:32 -05:00
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	Better debug output for SAMDataSource	2011-12-12 17:57:29 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Added test mode to PPP	2011-12-12 18:29:06 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00