gatk3的最后一个经典版本3.8

depristo 72ad8ded19 Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5837 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-22 18:43:48 +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	CalibrateGenotypeLikelihoods now emits a molten data set with REF and ALT alleles, so that GL calibration can be evaluated as a function of the REF/ALT bases. DigestTable is a stand-alone Rscript that digests the multi-GB molten data table into a tiny table that shows reported vs. empirical GLs, as a function of a variety of features of the data, like REF/ALT, comp GT, eval GT, and GL itself.	2011-05-21 14:02:30 +00:00
archive	Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway	2011-05-22 18:43:48 +00:00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	Removed old (and unused) reporting system, now that Kiran's VE reporting system is working. Refactors dictionary creation error messages into UserExceptions	2011-05-22 18:42:52 +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	Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway	2011-05-22 18:43:48 +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 now enabled by default in GATK build. The contract checking is automatically enabled when running tests and integrationtests. If you want to run the GATK with Contract checking enabled, add -javaagent:lib/cofoja.jar to your jvm args	2011-05-20 02:53:42 +00:00
ivy.xml	Factor out all testing dependencies into a separate test configuration and	2011-05-05 22:42:11 +00:00