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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 f0021a3533 Changes to the BTTC scala walker: 
- Updated to use the unified genotyper rather than ssg
 - Fixed a minor issue where the Unified Genotyper returns null
   and SSG would still return an object. isDefinitelyHomRef() now
   checks for null Unified Genotyper <Call list, meta data> pairs.
 - Tables output survive a diff with previous tables




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1872 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-10-18 18:09:25 +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 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 Updated MD5 2009-10-18 05:30:38 +00:00
packages moving IndelGenotyper out from playground 2009-09-25 19:43:53 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python simple monitor for watching pilot 1 call progress 2009-10-06 13:04:53 +00:00
scala/src Changes to the BTTC scala walker: 2009-10-18 18:09:25 +00:00
settings Bumping version of Picard for firehose compatibility. 2009-10-16 19:38:56 +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 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