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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
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depristo 5dce16a8f1 Better genotype concordance module. Code refactoring for clarity (please see below/after for educational purposes). Now reports variant sensitivity, concordance, and genotype error rate by default. Also aggregates this data across all samples, so you get a per sample and overall stats for each of these in the allSamples row. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3265 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-04-28 13:10:11 +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 Better genotype concordance module. Code refactoring for clarity (please see below/after for educational purposes). Now reports variant sensitivity, concordance, and genotype error rate by default. Also aggregates this data across all samples, so you get a per sample and overall stats for each of these in the allSamples row. 2010-04-28 13:10:11 +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 Renaming for consistency 2010-04-21 03:00:43 +00:00
perl Adding the post-processing indel filter to GATK 2010-04-27 14:43:39 +00:00
python some useful routines for working with project processing. madPipeline contains a bunch of useful routines for building pipelines that I finally put into one file. Let's just say that I'm really looking forward to the new pipeline system... 2010-04-26 12:34:04 +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 fixes for edge-cases when using reflections to find classes outside of the main jar. Will push as a patch to reflections 2010-04-27 17:46:46 +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 fixes for edge-cases when using reflections to find classes outside of the main jar. Will push as a patch to reflections 2010-04-27 17:46:46 +00:00