gatk3的最后一个经典版本3.8

hanna 773a72e6ea An initial fix for performance issues when filtering UG with new StratifiedAlignmentContext. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3724 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-07 01:07:46 +00:00
R	useful routines for R	2010-06-30 16:38:49 +00:00
archive	Retiring multi-sample genotyper	2010-05-20 14:11:11 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	An initial fix for performance issues when filtering UG with new StratifiedAlignmentContext.	2010-07-07 01:07:46 +00:00
matlab	Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function	2009-11-30 20:02:25 +00:00
packages	Update to the latest rev of the picard sharding patch. Includes updates reflecting	2010-06-06 20:33:21 +00:00
perl	Updated to reflect Mark's renaming binge	2010-06-30 22:48:42 +00:00
python	misc. useful updates to python library	2010-06-30 16:33:32 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	Checking in a simplistic VR qscript file for posterity's sake	2010-07-01 18:53:17 +00:00
settings	Rev Picard with new IndexedFastaSequenceFile patch.	2010-07-01 03:05:43 +00:00
shell	a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype.	2010-07-06 18:33:28 +00:00
testdata	and add changes to the vcf used in testing	2010-06-25 02:56:02 +00:00
LICENSE	Adding a license to the root directory in case BOSC checks for one. Has the	2010-04-20 16:04:29 +00:00
build.xml	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00
ivy.xml	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00