gatk3的最后一个经典版本3.8

alecw 2cf21317f9 Create package that contains just what Picard needs. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2282 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-07 21:22:07 +00:00
R	Histogram of covariate values now goes from 0 to max value which makes it look nicer in most cases.	2009-12-04 14:44:03 +00:00
archive	More archiving (with permission from Andrey) plus a move to core.	2009-12-03 15:40:27 +00:00
c	Add a Unix-standard version number to the file.	2009-11-23 20:07:17 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Cleanup results of bad merge.	2009-12-07 19:30:49 +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	Create package that contains just what Picard needs.	2009-12-07 21:22:07 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	minor improvements to snp selector	2009-12-07 03:37:14 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala/src	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00
settings	Push version number of picard-private-parts	2009-11-25 19:28:57 +00:00
shell	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00
testdata	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
build.xml	Move some files around to reflect our growing help infrastructure.	2009-12-07 19:23:12 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00