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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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aaron bca894ebce Adding the intial changes for the new Genotyping interface. The bullet points are: 
- SSG is much simpler now
- GeliText has been added as a GenotypeWriter
- AlleleFrequencyWalker will be deleted when I untangle the AlleleMetric's dependance on it
- GenotypeLikelihoods now implements GenotypeGenerator, but could still use cleanup

There is still a lot more work to do, but this is a good initial check-in.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1335 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-07-29 19:43:59 +00:00
R Updated python files 2009-07-07 14:15:39 +00:00
c Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java Adding the intial changes for the new Genotyping interface. The bullet points are: 2009-07-29 19:43:59 +00:00
packages Added indel cleaner and quality scores recalibrator to the GATK package. 2009-07-24 16:20:38 +00:00
perl sortByRef now supports x:y location syntax 2009-07-07 16:42:40 +00:00
python By default now writes output to JOBID.lsf.output instead of going to email -- based on recommendations from the cancer group 2009-07-28 13:18:58 +00:00
settings Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +00:00
shell Version 0.2.1 (released) of the TableRecalibrator 2009-06-25 22:50:55 +00:00
testdata Derive examples from real data. 2009-07-10 04:21:37 +00:00
build.xml added the abilty to build the jar's to a different location, like the following: 2009-07-23 04:06:58 +00:00
ivy.xml Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +00:00