gatk3的最后一个经典版本3.8

Ryan Poplin b5b9d745a7 New implementation of the GGA mode in the HaplotypeCaller ... -- We now inject the given alleles into the reference haplotype and add them to the graph. -- Those paths are read off of the graph and then evaluated with the appropriate marginalization for GGA mode. -- This unifies how Smith-Waterman is performed between discovery and GGA modes. -- Misc minor cleanup in several places.		2013-05-31 10:35:36 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	New implementation of the GGA mode in the HaplotypeCaller	2013-05-31 10:35:36 -04:00
public	New implementation of the GGA mode in the HaplotypeCaller	2013-05-31 10:35:36 -04:00
settings	Rev picard, sam-jdk, tribble, and variant to version 1.91.1453	2013-05-07 14:21:15 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
build.xml	Three squashed commits:	2013-05-31 00:26:50 -04:00
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