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gatk3的最后一个经典版本3.8
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ebanks 9b9744109c Mark's new unified calculation model is now officially implemented. 
Because it doesn't actually use EM, it's no longer a subclass of the EM model.

Note that you can't use it just yet because it doesn't actually emit calls (just prints to logger).  I need to deal with general UG output tomorrow.  Hold off until then, Mark, and then you can go wild.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1891 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-10-21 02:39:23 +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 Mark's new unified calculation model is now officially implemented. 2009-10-21 02:39:23 +00:00
packages Replaced SSG with UG in packaging utils. Minor performance and formatting improvements for ClipReads 2009-10-20 01:19:58 +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 Major code refactoring: 2009-10-20 14:58:04 +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