gatk3的最后一个经典版本3.8

ebanks e9eeed8c6f add wait id for 454 ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1678 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-22 01:41:58 +00:00
R	Get rid of unnecessary files for generating recalibration data.	2009-09-15 15:53:06 +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	After thinking about this a bit more, it makes sense to pull this functionality out of my walker and into the GenomeLocParser where everyone else can benefit from it...	2009-09-22 01:32:35 +00:00
packages	Get rid of unnecessary files for generating recalibration data.	2009-09-15 15:53:06 +00:00
perl	add wait id for 454	2009-09-22 01:41:58 +00:00
python	Fixes for VariantEval for genotyping mode	2009-09-18 21:01:43 +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