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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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ebanks a048f5cdf1 -Refactored JointEstimation code so that pooled calling will work 
-Use phred-scale for fisher strand test
-Use only 2N allele frequency estimation points



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2059 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-11-17 20:21:15 +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 -Refactored JointEstimation code so that pooled calling will work 2009-11-17 20:21:15 +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