Mauricio Carneiro 07128a2ad2 ReadUtils cleanup ... * Removed all clipping functionality from ReadUtils (it should all be done using the ReadClipper now) * Cleaned up functionality that wasn't being used or had been superseded by other code (in an effort to reduce multiple unsupported implementations) * Made all meaningful functions public and added better comments/explanation to the headers		2011-12-20 17:48:40 -05:00
..
R	Protect ourselves when iteration is present but there's only a single iteration in queueJobReport.R	2011-12-19 10:08:38 -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	ReadUtils cleanup	2011-12-20 17:48:40 -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	General improvements to Queue	2011-12-20 14:05:09 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00