gatk3的最后一个经典版本3.8

chartl 3d92e5a737 Initial commit of integration test(s) for CoverageStatistics, currently in progress [midway commit is for Matt] ... Modifications to CoverageStatistics - now includes and extends much of the behavior of DepthOfCoverage (per-base output, per-target output). Additional functionality (coverage without deletions, base counts, by read group instead of by sample) is upcoming. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2888 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-25 20:25:07 +00:00
R	Using bitmap() instead of png() since the former doesn't rely on X11.	2010-02-23 05:31:51 +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	Initial commit of integration test(s) for CoverageStatistics, currently in progress [midway commit is for Matt]	2010-02-25 20:25:07 +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	Since IntervalCleaner is gone for good, it is sensible to update the package to refer to the new IndelRealigner instead	2010-02-24 16:42:56 +00:00
perl	Allow no-call alleles to propagate through to the MAF file	2010-02-16 20:46:16 +00:00
python	Outputing annotated VCF to the current directory instead of attempting to write in the directory next to the original vcf.	2010-02-22 21:31:24 +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	adding a stripped down Tribble library for the start of integration	2010-02-17 21:29:25 +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	Fully qualify the target for the output file so that external build processes (aka firehose)	2010-01-26 23:06:30 +00:00
ivy.xml	adding a stripped down Tribble library for the start of integration	2010-02-17 21:29:25 +00:00