gatk-3.8

gatk3的最后一个经典版本3.8

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hanna ee421c106c Autogenerate .tar.bz2 with embedded version number. Misc formatting changes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2651 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-21 18:32:46 +00:00
R	Draft version of AnalyzeAnnotations which creates plots of cumulative TiTv ratio versus filter value per each annotation in the input VCF rod. Minor cleanup of recalibration walkers.	2010-01-18 20:47:10 +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	Alteration of PlinkToVCF to be much more flexible about parsing .ped file headers, which can have one of a number of different standard fields, and be in different orders.	2010-01-21 18:02:28 +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	Autogenerate .tar.bz2 with embedded version number. Misc formatting changes.	2010-01-21 18:32:46 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Valuable series of commands	2010-01-20 13:58:59 +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	Print out the current version number in the application header.	2010-01-19 21:58:36 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00