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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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ebanks fddca032bb Initial commit of v2.0 of the cleaner. DO NOT USE. (this means you, Chris) 
Cleaned up SW code and started moving over everything to use byte[] instead of String or char[].

Added a wrapper class for SAMFileWriter that allows for adding reads out of order.

Not even close to done, but I need to commit now to sync up with Andrey.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2712 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-01-27 21:36:42 +00:00
R AnalyzeAnnotations creates a plot of dbsnp rate as a function of the annotations. 2010-01-27 21:08:33 +00:00
archive Making a copy here before changing the live copy 2010-01-27 20:44:15 +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 Initial commit of v2.0 of the cleaner. DO NOT USE. (this means you, Chris) 2010-01-27 21:36:42 +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 Fix the dreaded 'can't use fully qualified symlinks on the ftp server' gotcha. 2010-01-27 20:55:48 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python A collection of python objects that are useful for VCF validation. Use 'em or don't. 2010-01-25 18:44:10 +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 New Picard and SAM-JDK with automatic sequence name truncation 2010-01-11 20:49:13 +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 Fully qualify the target for the output file so that external build processes (aka firehose) 2010-01-26 23:06:30 +00:00
ivy.xml New VariantFiltration. 2009-11-20 19:50:26 +00:00