gatk3的最后一个经典版本3.8

aaron 844cb2ed33 fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric! ... Also putting more tolerance into the timing on the tibble index tests (that check to make sure we're deleting out of date indexes, and not deleting perfectly good indexes). It seems that some of the farm nodes aren't great with a stopwatch. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3674 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-29 21:38:55 +00:00
R	This replaces tearsheet.r, neatens up graphics, and allows the script to be used in R's interactive environment	2010-06-24 01:02:58 +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	fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric!	2010-06-29 21:38:55 +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	Updates to not depend on an environment variable to figure out where libraries are (helpful for installation at the Sanger).	2010-06-28 15:46:41 +00:00
python	Fixed error message	2010-06-28 14:50:28 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	Added "-bsubWait" where Queue waits for all the jobs to exit before exiting.	2010-06-28 19:52:17 +00:00
settings	Rev'ing Tribble with a special version that has excluded VCF 3.3	2010-06-25 18:20:51 +00:00
shell	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +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