gatk3的最后一个经典版本3.8

Eric Banks 2f5ef6db44 New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. ... * This version inherits from the original SW implementation so it can use the same matrix creation method. * A bunch of refactoring was done to the original version to clean it up a bit and to have it do the right thing for indels at the edges of the alignments. * Enum added for the overhang strategy to use; added implementation for the INDEL version of this strategy. * Lots of systematic testing added for this implementation. * NOT HOOKED UP TO HAPLOTYPE CALLER YET. Committing so that people can play around with this for now.		2013-05-13 09:36:39 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.	2013-05-13 09:36:39 -04:00
public	New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.	2013-05-13 09:36:39 -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	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -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