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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 4fbb6d05d0 Refactoring. Push the revisions to the common aligner interface down into 
the aligner base classes.  Hack the managed implementation to support the
new interface.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2103 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-11-20 17:08:09 +00:00
R R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design. 2009-09-22 18:10:14 +00:00
c Refactoring. Push the revisions to the common aligner interface down into 2009-11-20 17:08:09 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java Refactoring. Push the revisions to the common aligner interface down into 2009-11-20 17:08:09 +00:00
packages Picard-private with classes for reading Picard dbSNP binary file 2009-11-19 17:24:28 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python cleanup of SNP selector -- ready for some additional testing 2009-11-13 21:46:31 +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 Update xml descriptor with proper version number. 2009-11-19 17:32:22 +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 GSA-182: Adding support for BED interval files. 2009-10-06 02:45:31 +00:00
build.xml Build aligner as separate jar file. 2009-11-13 22:29:29 +00:00
ivy.xml Extract and include only the Tim Fennell-approved parts of picard private. 2009-11-13 19:42:33 +00:00