gatk3的最后一个经典版本3.8

bthomas b4f6f54502 Reorganizing the way interval arguments are processed ... Most of the changes occur in GenomeAnalysisEngine.java and GenomeLocParser.java: -- parseIntervalRegion and parseGenomeLocs combined into parseIntervalArguments -- initializeIntervals modified -- some helper functions deprecated for cleanliness Includes new set of unit tests, GenomeAnalysisEngineTest.java New restrictions: -- all interval arguments are now checked to be on the reference contig -- all interval files must have one of the following extensions: .picard, .bed, .list, .intervals, .interval_list git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3106 348d0f76-0448-11de-a6fe-93d51630548a		2010-04-01 12:47:48 +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	Reorganizing the way interval arguments are processed	2010-04-01 12:47:48 +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	This is a python job dispatcher I've been using, which builds on Mark's FarmJob utility, and an example script of how I'm using it. Basically I wrote it to smartly break up analysis over an interval list, givin a maximum number of bases per job, a list of available queues, and a limit on each queue. It handles going over these limits in three ways:	2010-03-31 19:53:13 +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	Another round of cleanup and simplification in Picard -- Picard's unit tests	2010-03-31 01:02:59 +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	implementing a clean way to import the template files into the GATK jar (they should not always get bundled). All further resources should be added to the gatk.resources path id in the build script.	2010-03-30 04:20:19 +00:00
ivy.xml	adding a dependency that I forgot.	2010-03-18 13:32:37 +00:00