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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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chartl 7d6d114ab5 Additions: 
@NQSMismatchCovariantWalker - Walks along the gene calculating the table     
    # NQS
    # Q score
    # mismatches at non-dbsnp sites
    # total number of bases at non-dbsnp sites

And prints it out at the end.

Changes:

@PooledGenotypeConcordance now works. Takes a path to a file listing a bunch of hapmap IDs in whatever pool we want to check, reads those in, and checks for concordance by name.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1614 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-09-14 20:12:04 +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 Additions: 2009-09-14 20:12:04 +00:00
packages SSG now in early access 2009-09-10 16:45:19 +00:00
perl finished up modularized pipeline; needs some testing but is generally done. 2009-09-14 02:41:57 +00:00
python Framework for ROD walkers -- totally experiment and not working right now 2009-09-12 19:13:15 +00:00
scala/src support for scala walkers 2009-08-28 00:15:01 +00:00
settings Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +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 Framework for ROD walkers -- totally experiment and not working right now 2009-09-12 19:13:15 +00:00
build.xml changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script. 2009-09-10 04:31:33 +00:00
ivy.xml Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +00:00