gatk3的最后一个经典版本3.8

Mark DePristo 315d25409f Improvement to RecalDatum and VisualizeContextTree ... -- Reorganize functions in RecalDatum so that error rate can be computed indepentently. Added unit tests. Removed equals() method, which is a buggy without it's associated implementation for hashcode -- New class RecalDatumTree based on QualIntervals that inherits from RecalDatum but includes the concept of sub data -- VisualizeContextTree now uses RecalDatumTree and can trivially compute the penalty function for merging nodes, which it displays in the graph		2012-07-31 08:11:04 -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	Improvement to RecalDatum and VisualizeContextTree	2012-07-31 08:11:04 -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