gatk-3.8

gatk3的最后一个经典版本3.8

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aaron 7467ec2fd6 updating the reflections library; Matt found a problem where the reflections library doesn't sort out non-java objects from the classpath (affects only OS X so far). I'll push back the changes to the reflections library people. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3307 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-06 02:08:41 +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	First pass at liftover tool. Passing buck over to Aaron...	2010-05-05 20:38:19 +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	First pass at liftover tool. Passing buck over to Aaron...	2010-05-05 20:38:19 +00:00
perl	Adding the post-processing indel filter to GATK	2010-04-27 14:43:39 +00:00
python	Added - Q&D script to gather verbose bed files to a VCF.	2010-05-05 02:49:16 +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 the reflections library; Matt found a problem where the reflections library doesn't sort out non-java objects from the classpath (affects only OS X so far). I'll push back the changes to	2010-05-06 02:08:41 +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
LICENSE	Adding a license to the root directory in case BOSC checks for one. Has the	2010-04-20 16:04:29 +00:00
build.xml	fixed the build	2010-04-09 13:03:31 +00:00
ivy.xml	updating the reflections library; Matt found a problem where the reflections library doesn't sort out non-java objects from the classpath (affects only OS X so far). I'll push back the changes to	2010-05-06 02:08:41 +00:00