gatk3的最后一个经典版本3.8

Mark DePristo e00ed8bc5e Cleanup BQSR classes ... -- Moved most of BQSR classes (which are used throughout the codebase) to utils.recalibration. It's better in my opinion to keep commonly used code in utils, and only specialized code in walkers. As code becomes embedded throughout GATK its should be refactored to live in utils -- Removed unncessary imports of BQSR in VQSR v3 -- Now ready to refactor QualQuantizer and unit test into a subclass of RecalDatum, refactor unit tests into RecalDatum unit tests, and generalize into hierarchical recal datum that can be used in QualQuantizer and the analysis of adaptive context covariate -- Update PluginManager to sort the plugins and interfaces. This allows us to have a deterministic order in which the plugin classes come back, which caused BQSR integration tests to temporarily change because I moved my classes around a bit.		2012-07-31 08:11:03 -04:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	Cleanup BQSR classes	2012-07-31 08:11:03 -04:00
public	Cleanup BQSR classes	2012-07-31 08:11:03 -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