gatk3的最后一个经典版本3.8

kshakir 08f0509a5c Disabling the queue/pipeline package by default so that scala code can build. If it's not going to be fixed the package should be removed. If it is going to be fixed this patch to build.xml should be reverted. ... Also added the old model of indel calling to the FCP. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5749 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-04 12:17:33 +00:00
R	Adding tranche plot generation back to VQSR	2011-05-03 19:26:26 +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	Bring back from the dead the old likelihoods model for indels, which has worse performance but is about 4x faster. Enabled with argument -GSA_PRODUCTION_ONLY in UG	2011-05-03 22:38:33 +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	Disabling the queue/pipeline package by default so that scala code can build. If it's not going to be fixed the package should be removed. If it is going to be fixed this patch to build.xml should be reverted.	2011-05-04 12:17:33 +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	ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard.	2011-02-21 14:02:41 +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	Disabling the queue/pipeline package by default so that scala code can build. If it's not going to be fixed the package should be removed. If it is going to be fixed this patch to build.xml should be reverted.	2011-05-04 12:17:33 +00:00
ivy.xml	Updating to apache commons math v2.	2011-04-26 17:31:49 +00:00