gatk3的最后一个经典版本3.8

Mark DePristo 45603f58cd Refactoring and unit testing GenomeLocParser ... -- Moved previously inner class to MRUCachingSAMSequenceDictionary, and unit test to 100% coverage -- Fully document all functions in GenomeLocParser -- Unit tests for things like parsePosition (shocking it wasn't tested!) -- Removed function to specifically create GenomeLocs for VariantContexts. The fact that you must incorporate END attributes in the context means that createGenomeLoc(Feature) works correctly -- Depreciated (and moved functionality) of setStart, setStop, and incPos to GenomeLoc -- Unit test coverage at like 80%, moving to 100% with next commit		2013-01-30 09:47:47 -05:00
licensing	Refrain from pushing symlinks into the repo... not all filesystems treat it correctly	2013-01-22 15:18:19 -07:00
protected/java	Cleanup, document, and unit test ActiveRegion	2013-01-30 09:47:12 -05:00
public	Refactoring and unit testing GenomeLocParser	2013-01-30 09:47:47 -05:00
settings	Final r119 tribble jar	2012-11-02 14:30:33 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Remove the ability to package GATK/Queue Lite from the build system	2013-01-28 02:42:37 -05:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	ReadBackedPileup cleanup	2013-01-11 15:17:18 -05:00