gatk3的最后一个经典版本3.8

chartl 3a4844ebde Additional partition types into DepthOfCoverage: ... - Sequencing Center - Platform - Sample by Center - Sample by Platform - Sample by Platform by Center <---- needed for analysis I'm doing The fact that the latter three needed their own partition types, rather than being dictatable from the command line, combined with the new hierarchical traversal types, and new output formatting engine, suggest that DepthOfCoverageV3 is about ready to be retired in favor of a newer, sleeker version. For now, this will do. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4193 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-02 19:30:03 +00:00
R	Better reporting and now with a special mode for listing exceptions	2010-09-01 16:19:51 +00:00
archive	Cleaning up playground utils and tests	2010-08-27 01:25:47 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +00:00
doc	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
java	Additional partition types into DepthOfCoverage:	2010-09-02 19:30:03 +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	Enabling support for any scala used in QScripts.	2010-08-17 22:05:56 +00:00
perl	Removing the obsolete --hapmap and --hapmap_chip options	2010-08-31 16:57:05 +00:00
python	More robust analysis tool	2010-09-01 20:24:04 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Queue scripts for recalibration and running nSample UG jobs pre and dynamic merging	2010-09-01 20:23:37 +00:00
settings	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
shell	Useful script to see the status of gsa computing resources. Crontab'd and will be arriving as email at 8 am	2010-08-07 12:36:28 +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	up the test mem. from 2g to 4g; we're currently hitting the 2g in aggregate across some of the larger tests	2010-08-27 01:39:05 +00:00
ivy.xml	Okay, finally done with VCF compression. Now:	2010-08-24 16:36:54 +00:00