gatk3的最后一个经典版本3.8

David Roazen 5baf906c28 Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists ... -The algorithm for finding the intersection of two sets of intervals relies on the sortedness of the intervals within each set, but the engine was not sorting the intervals before attempting to find the intersection. -The result was that if one or both interval lists was unsorted / lexicographically sorted, we would often fail to find the intersection correctly. -Now the IntervalBinding sorts all sets of intervals before returning them, solving the problem. -Added an integration test for this case. GSA-909 #resolve		2013-04-02 14:01:52 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Two changes to HC GGA mode to make it more like the UG.	2013-04-01 10:20:23 -04:00
public	Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists	2013-04-02 14:01:52 -04:00
settings	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00