gatk3的最后一个经典版本3.8

ebanks babb9fb825 snp cluster filter should ignore ref calls when determining the clusters ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3093 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-29 17:57:33 +00:00
R	Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics	2010-03-29 13:32:00 +00:00
archive	moving older versions of the oneoff project to archive, bye-bye	2010-02-04 19:46:27 +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	snp cluster filter should ignore ref calls when determining the clusters	2010-03-29 17:57:33 +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	Add CoverageStatistics	2010-03-29 15:45:53 +00:00
perl	Passing just the single alternate allele to the converted maf on the recommendation of mike lawrence and kiran.	2010-03-17 19:08:37 +00:00
python	Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics	2010-03-29 13:32:00 +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	Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of	2010-03-29 03:21:27 +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
templates/VE2	First go of the new output system for VE2. There are three different report types supported right now (Table, Grep, CSV), which can be	2010-03-27 03:59:32 +00:00
testdata	a small dbsnp file for Tribble testing	2010-02-18 18:12:55 +00:00
build.xml	In the new sharding system, if no read group is present, hallucinate one. Added	2010-03-07 23:01:34 +00:00
ivy.xml	adding a dependency that I forgot.	2010-03-18 13:32:37 +00:00