gatk3的最后一个经典版本3.8

aaron b5f6f54968 Almost done removing any trace of the old Variation and Genotype interfaces. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3202 348d0f76-0448-11de-a6fe-93d51630548a		2010-04-20 14:52:15 +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	more clean-up: moving AlleleBalanceInspector to archive.	2010-04-16 20:53:33 +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	Almost done removing any trace of the old Variation and Genotype interfaces.	2010-04-20 14:52:15 +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	Adding VE modules to package	2010-04-16 14:44:06 +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	Marginally more useful output	2010-04-20 14:45:14 +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	Updating picard -- switching to Alec's more robust fix for gzip decompression issue	2010-04-12 19:56:45 +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	a small dbsnp file for Tribble testing	2010-02-18 18:12:55 +00:00
build.xml	fixed the build	2010-04-09 13:03:31 +00:00
ivy.xml	Modified the report system based on Ryan's feedback: tables are now created independently to avoid the permutation problem when they were all compressed in rows, and removed our dependency on FreeMarker. The Grep format stays the same.	2010-04-07 20:39:55 +00:00