Mauricio Carneiro 62a2e335bc Changing HardClipper contract to allow UNMAPPED reads ... shifted the contract to functions that operate on reference based coordinates. The clipper should do the right thing with unmapped reads, but it needs more testing (Ryan is using it at the moment and says it works). Will write some unit tests.		2011-12-15 11:08:19 -05:00
..
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	Changing HardClipper contract to allow UNMAPPED reads	2011-12-15 11:08:19 -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