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gatk3的最后一个经典版本3.8
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ebanks 04fe50cadd *** We no longer have a separate model for the single-sample case. *** 
For now, a single sample input will be special-cased in the EM model - but that will change when the EM model degenerates to the single sample output with a single sample as input.  For now, the EM code for multi-samples isn't finished; I'm planning on checking that in soon.

The SingleSampleIntegrationTest now uses the UnifiedCaller instead of SSG, and so should all of you.  More on that in a separate email.
Other minor cleanups added too.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1785 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-10-08 14:08:57 +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 *** We no longer have a separate model for the single-sample case. *** 2009-10-08 14:08:57 +00:00
packages moving IndelGenotyper out from playground 2009-09-25 19:43:53 +00:00
perl add wait id for 454 2009-09-22 01:41:58 +00:00
python simple monitor for watching pilot 1 call progress 2009-10-06 13:04:53 +00:00
scala/src support for scala walkers 2009-08-28 00:15:01 +00:00
settings epic fail! 2009-09-30 20:49:42 +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