gatk3的最后一个经典版本3.8

Eric Banks dadcfe296d Reworking of the dangling tails merging code. ... We now run Smith-Waterman on the dangling tail against the corresponding reference tail. If we can generate a reasonable, low entropy alignment then we trigger the merge to the reference path; otherwise we abort. Also, we put in a check for low-complexity of graphs and don't let those pass through. Added tests for this implementation that checks exact SW results and correct edges added.		2013-06-11 12:53:04 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Reworking of the dangling tails merging code.	2013-06-11 12:53:04 -04:00
public	Reworking of the dangling tails merging code.	2013-06-11 12:53:04 -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	Restore scala compilation by default in build.xml	2013-05-31 11:28:29 -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