gatk3的最后一个经典版本3.8

hanna 022601b1a5 Warnings for walkers w/o Javadoc. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2683 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-25 20:34:50 +00:00
R	AnalyzeAnnotations now outputs plots with log x-axis in addition to standard x-axis so things like DP and MQ0 are easier to see. AnalyzeAnnotations now skips over all annotations that aren't floating point values. Recalibrator now warns users if PL tags are missing and so therefore it is reverting to illumina.	2010-01-25 19:39:18 +00:00
archive	Home for retired duplicateQuals analysis utility	2010-01-06 15:05:00 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Warnings for walkers w/o Javadoc.	2010-01-25 20:34:50 +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	Temporary solution: add the commons logging implementation to the VariantFiltration package. Downstream solution is described in GSA-262.	2010-01-23 01:46:18 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	A collection of python objects that are useful for VCF validation. Use 'em or don't.	2010-01-25 18:44:10 +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	New Picard and SAM-JDK with automatic sequence name truncation	2010-01-11 20:49:13 +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	Warnings for walkers w/o Javadoc.	2010-01-25 20:34:50 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00