gatk3的最后一个经典版本3.8

Mark DePristo e1bba91836 Ready for full-scale evaluation adaptive BQSR contexts ... -- VisualizeContextTree now can write out an equivalent BQSR table determined after adaptive context merging of all RG x QUAL x CONTEXT trees -- Docs, algorithm descriptions, etc so that it makes sense what's going on -- VisualizeContextTree should really be simplified when into a single tool that just visualize the trees when / if we decide to make adaptive contexts standard part of BQSR -- Misc. cleaning, organization of the code (recalibation tests were in private but corresponding actual files were public)		2012-08-03 16:02:53 -04:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	Fixed 2 haplotype caller unit tests: a) new interface for addReadLikelihoods() including read counts, b) disable test that test basic DeBruijn graph assembly, not ready yet	2012-08-03 14:26:51 -04:00
public	Ready for full-scale evaluation adaptive BQSR contexts	2012-08-03 16:02:53 -04:00
settings	Removed Categories.	2012-07-25 13:46:24 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	Remove reference dependence in BCF2Codec	2012-07-25 08:56:38 -04:00
ivy.xml	V1 of tool to visualize the quality score information in the context covariates	2012-07-31 08:11:02 -04:00