gatk3的最后一个经典版本3.8

kshakir 4d08d39849 Moved some of the java to scala conversions from production to test code as it's not needed in production and slows down the code. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5769 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-05 04:11:15 +00:00
R	Status messages to user added	2011-05-04 20:10:47 +00:00
analysis/depristo	Scripts for creating S3 IGV account	2011-04-02 13:39:47 +00:00
archive	Moving GLF code to archive	2011-01-15 22:42:42 +00:00
c	Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.	2010-12-17 14:49:15 +00:00
chainFiles	Adding chain files for Mark. Tested by lifting over back and forth between builds. Note that they comprise only the standard contigs so no _randoms or GL000xxx.1s.	2011-04-22 14:53:15 +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	Fixed O(N^2) operation when scattering interval files.	2011-05-05 03:32:35 +00:00
lua	forgot to remove a debug line.	2011-02-15 16:25:48 +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	Added JavaMail dependencies to Queue package since bcel wasn't picking them up.	2011-04-23 20:48:40 +00:00
perl	Quit immediately with an error message if any of the individual steps fails.	2011-04-22 13:23:33 +00:00
python	A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles)	2011-03-21 16:11:55 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Moved some of the java to scala conversions from production to test code as it's not needed in production and slows down the code.	2011-05-05 04:11:15 +00:00
settings	Revbump Picard dependencies at Tim/Kathleen's request. Exclude anonymous	2011-04-27 20:38:05 +00:00
shell	Useful utility for looking at the file size of GSA file systems	2011-04-02 03:47:27 +00:00
testdata	Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting	2011-05-04 13:56:01 +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	Removing QPipeline directory as there's no one to support it at the moment.	2011-05-04 18:36:02 +00:00
ivy.xml	Updating to apache commons math v2.	2011-04-26 17:31:49 +00:00