gatk-3.8

gatk3的最后一个经典版本3.8

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chartl 5cf1d6c104 Bugfix - this walker was never changed to work with the new PoolUtils methods after those methods were changed to return ReadOffsetQuad objects rather than nested pairs. This broke the build :(. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1608 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-13 19:39:23 +00:00
R	Updated python files	2009-07-07 14:15:39 +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	Bugfix - this walker was never changed to work with the new PoolUtils methods after those methods were changed to return ReadOffsetQuad objects rather than nested pairs. This broke the build :(.	2009-09-13 19:39:23 +00:00
packages	SSG now in early access	2009-09-10 16:45:19 +00:00
perl	2nd stab at creating a pipeline [not quite finished yet].	2009-09-13 05:53:18 +00:00
python	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +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