gatk-3.8

gatk3的最后一个经典版本3.8

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ebanks bc98ac1e74 Adding a TODO for future consideration git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5821 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-19 15:02:23 +00:00
R	Removing requirement of providing known track in VQSR for the non-humans. Updating placement of legend on tranche plot.	2011-05-05 20:24:06 +00:00
analysis/depristo	Added splitContextByReadGroup() and fixed bug in getPileupForReadGroup() that resulted in a NPE when no reads where present for a read group.	2011-05-15 17:36:07 +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	Renaming for consistency	2011-05-10 16:36:39 +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	Adding a TODO for future consideration	2011-05-19 15:02:23 +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	Quick small updates:	2011-05-18 20:08:39 +00:00
settings	Contracts for Java (http://code.google.com/p/cofoja/) infrastructure enabled. No piece of code actually uses this, so it's possible to remove easily. Does not build by default (you must modify build.xml). Really an intermediate commit so I can play around with the system in my java classes and revert safely. Very much looking forward to DVCS	2011-05-18 18:05:59 +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	Contracts for Java (http://code.google.com/p/cofoja/) infrastructure enabled. No piece of code actually uses this, so it's possible to remove easily. Does not build by default (you must modify build.xml). Really an intermediate commit so I can play around with the system in my java classes and revert safely. Very much looking forward to DVCS	2011-05-18 18:05:59 +00:00
ivy.xml	Factor out all testing dependencies into a separate test configuration and	2011-05-05 22:42:11 +00:00