Eric Banks 3e7714629f Scrapped the whole idea of an int/long as an index into the ACset: with lots of alternate alleles we run into overflow issues. Instead, simply use the ACcounts array as the hash key since it is unique for each AC conformation. To do this, it needed to be wrapped inside an object so hashcode() would work.		2011-12-08 23:50:54 -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	Scrapped the whole idea of an int/long as an index into the ACset: with lots of alternate alleles we run into overflow issues. Instead, simply use the ACcounts array as the hash key since it is unique for each AC conformation. To do this, it needed to be wrapped inside an object so hashcode() would work.	2011-12-08 23:50:54 -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