Eric Banks 4aebe99445 Need to use longs for the set index (because we can run out of ints when there are too many alternate alleles). Integration tests now use the multiallelic implementation.		2011-12-08 15:31:02 -05:00
..
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	Need to use longs for the set index (because we can run out of ints when there are too many alternate alleles). Integration tests now use the multiallelic implementation.	2011-12-08 15:31:02 -05:00
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	Queue now outputs a GATK-like header with version number, build timestamp, etc.	2011-11-23 14:28:35 -05:00
testdata	Testdata for IntervalStratification	2011-11-10 11:08:34 -05:00