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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 fe6d810515 Some basic commits that I've been sitting on for a while now: 
@ PooledGenotypeConcordance - changes to output, now also reports false-negatives and false-positives as interesting sites. It's been like this in my directory for ages, just never committed.

@NQSExtendedGroupsCovariantWalker - change for formatting.

@NQSTabularDistributionWalker - breaks out the full (window_size)-dimensional empirical error rate distribution by the window. So if you've got a window of size 3; the quality score sequences 22 25 23 and 22 25 24 have their own bins (each of the 40^3 sequences get one) for match and mismatch counts.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1730 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-09-25 19:35:50 +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 Some basic commits that I've been sitting on for a while now: 2009-09-25 19:35:50 +00:00
packages Fail for missing resource files / scripts. 2009-09-22 21:31:01 +00:00
perl add wait id for 454 2009-09-22 01:41:58 +00:00
python Detects unmapped (no bai) bam files and doesn't blow up 2009-09-25 12:56:28 +00:00
scala/src support for scala walkers 2009-08-28 00:15:01 +00:00
settings Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +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 Framework for ROD walkers -- totally experiment and not working right now 2009-09-12 19:13:15 +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