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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%
JavaScript 0.1%
 
 
 
 
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hanna d9398dc347 Remove some of the restrictions on getStart() and getStop(); getStart() and getStop() 
now do the minimum validation rather than the more rigorous only-within-the-contig-bounds 
header validation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3027 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-03-17 19:39:30 +00:00
R Removed the StingException when mkdir fails for Sendu in AnalyzeCovariates. Incremental updates to VariantOptimizer. 2010-03-16 19:45:02 +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 Remove some of the restrictions on getStart() and getStop(); getStart() and getStop() 2010-03-17 19:39:30 +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 removing a reference to the VCFValidator, which is gone. 2010-03-11 21:32:17 +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 automatic generation of individual and individual set import files 2010-03-15 10:36:33 +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 In the new sharding system, if no read group is present, hallucinate one. Added 2010-03-07 23:01:34 +00:00
ivy.xml adding a stripped down Tribble library for the start of integration 2010-02-17 21:29:25 +00:00