gatk-3.8

gatk3的最后一个经典版本3.8

Go to file

hanna 3b440e0dbc Add a taglet to allow users to override the display name in command-line help. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2270 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-06 04:12:10 +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	Add a taglet to allow users to override the display name in command-line help.	2009-12-06 04:12:10 +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	Update the location of the DepthOfCoverage tool in the packaging system.	2009-12-03 19:11:53 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Syzygy has a default LOD score of 0.91 on bases with no coverage, this is problematic. Set the minimum lod threshold to 1 because I just don't want to see that codswallop.	2009-12-04 23:29:14 +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	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00