gatk-3.8

gatk3的最后一个经典版本3.8

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ebanks 0748d80baa Added a convenience method in rodDbSNP to deal with Andrey's changes to the rod. Now you can just ask for the first real SNP rod from the list and not have to think about how it works. CountCovariates uses it. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1688 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-22 20:15:40 +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	Added a convenience method in rodDbSNP to deal with Andrey's changes to the rod. Now you can just ask for the first real SNP rod from the list and not have to think about how it works.	2009-09-22 20:15:40 +00:00
packages	Package tool doesn't provide an error if classes listed in the package are not found, and classes were moved from playground to core.	2009-09-22 15:06:45 +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