gatk3的最后一个经典版本3.8

chartl 0eb777612a Swap "." over to VCFConstants.MISSING_DEPTH_v3 ... Why v3, you ask? Why not? Simply because v2 was a String so old and clunky, the sun would fizzle out and grow cold before any VCF could be successfully parsed. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4421 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-04 13:41:41 +00:00
R	* Added an R package, "gsalib", providing a place to store common, useful, documented R methods. To use this module, you must follow three steps:	2010-10-04 00:27:59 +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	Swap "." over to VCFConstants.MISSING_DEPTH_v3	2010-10-04 13:41:41 +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	Removed the SequenomValidationConvertor and renamed it VariantValidationAssessor since it no longer handles ped/sequenom files (but instead works on vcfs/variantcontexts). Updated all of the wiki docs, including adding instructions on how to convert ped files to vcf, a la Shaun Purcell. We now officially no longer support ped files everyone. Other misc cleanup in the code.	2010-10-04 02:11:38 +00:00
perl	Obsoleted by VariantReport.R	2010-10-04 01:00:59 +00:00
python	clean-up the docs a little	2010-09-29 05:02:41 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Sigh. Fix the source of even more UserErrors in the phone home directory: make sure to gunzip the beagle files before passing them into the conversion walker...	2010-10-01 03:28:36 +00:00
settings	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
shell	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +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	Renamed conflicting 'package.dir' in build.xml to 'package.xml.dir'.	2010-10-04 00:46:47 +00:00
ivy.xml	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00