gatk3的最后一个经典版本3.8

Mark DePristo 8d9b0f1bd5 Restructure ActivityProfiler into root class ActivityProfile and derived class BandPassActivityProfile ... -- Required before I jump in an redo the entire activity profile so it's can be run imcrementally -- This restructuring makes the differences between the two functionalities clearer, as almost all of the functionality is in the base class. The only functionality provided by the BandPassActivityProfile is isolated to a finalizeProfile function overloaded from the base class. -- Renamed ActivityProfileResult to ActivityProfileState, as this is a clearer indication of its actual functionality. Almost all of the misc. walker changes are due to this name update -- Code cleanup and docs for TraverseActiveRegions -- Expanded unit tests for ActivityProfile and ActivityProfileState		2013-01-23 13:45:21 -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	Restructure ActivityProfiler into root class ActivityProfile and derived class BandPassActivityProfile	2013-01-23 13:45:21 -05:00
public	Restructure ActivityProfiler into root class ActivityProfile and derived class BandPassActivityProfile	2013-01-23 13:45:21 -05:00
settings	Final r119 tribble jar	2012-11-02 14:30:33 -04:00
.gitignore	adding some directories to gitignore	2012-09-27 11:09:41 -04:00
build.xml	Updating Queue maven version to 0.0.2	2013-01-10 13:46:49 -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