gatk-3.8

gatk3的最后一个经典版本3.8

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chartl 4ad46590a3 Changes to PooledGenotypeConcordance: Additional output & better output formatting. It has now undergone a good five hours of testing; and for pools of size 1 outputs exactly the same statistics as GenotypeConcordance (when GenotypeConcordance is modified to do nothing on reference='N'); and for pools of many sizes outputs close to the expected (by genetics) statistics. Looks like this is working properly. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1642 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-16 21:45:01 +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	Changes to PooledGenotypeConcordance:	2009-09-16 21:45:01 +00:00
packages	Get rid of unnecessary files for generating recalibration data.	2009-09-15 15:53:06 +00:00
perl	perl script to make batching jobs easier	2009-09-16 19:02:46 +00:00
python	Automated parsing stats from VariantEval and outputting stats to "*.oneline_stats" files; needed to do larger culling of predictions vs. actual SNP call for Pilot 3 lanes	2009-09-14 23:40:11 +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