gatk3的最后一个经典版本3.8

Mark DePristo b3ecfbfce8 Refactor LIBS into component parts, expand unit tests, some code cleanup ... -- Split out all of the inner classes of LIBS into separate independent classes -- Split / add unit tests for many of these components. -- Radically expand unit tests for SAMRecordAlignmentState (the lowest level piece of code) making sure at least some of it works -- No need to change unit tests or integration tests. No change in functionality. -- Added (currently disabled) code to track all submitted reads to LIBS, but this isn't accessible or tested		2013-01-11 15:17:16 -05:00
licensing	Cleaning CRLF terminations in the licenses	2013-01-10 17:06:29 -05:00
protected/java	Merged bug fix from Stable into Unstable	2013-01-11 11:05:27 -05:00
public	Refactor LIBS into component parts, expand unit tests, some code cleanup	2013-01-11 15:17:16 -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	Updating to latest google caliper code	2013-01-11 15:17:16 -05:00