gatk3的最后一个经典版本3.8

ebanks a32470cea1 Deal with the fact that walkers can call UG's init/map functions directly. ... We need to filter contexts in that case since the calling walkers don't get UG's traversal-level filters. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1848 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-15 02:31:45 +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	Deal with the fact that walkers can call UG's init/map functions directly.	2009-10-15 02:31:45 +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	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