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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 b68d6e06b7 Rollback of the previous "fix" and implementation of the real fix. 
We totally *do* want to annotate the call if called by another walker. Totally boneheaded misenterpretation of what the code was doing -- Eric, please forgive me for being an idiot.

Instead, change the StingException to what it really should be -- an IllegalStateException, which is not coincidentally already handled by the calling function. 



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2067 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-11-18 06:09:24 +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 Bulletproofing code. If errors are encountering during the run, turn them 2009-11-14 22:57:16 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java Rollback of the previous "fix" and implementation of the real fix. 2009-11-18 06:09:24 +00:00
packages Extract and include only the Tim Fennell-approved parts of picard private. 2009-11-13 19:42:33 +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 Extract and include only the Tim Fennell-approved parts of picard private. 2009-11-13 19:42:33 +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