gatk3的最后一个经典版本3.8

Mark DePristo 80d9b7011c Complete rewrite of low-level machinery of LIBS, not hooked up ... -- AlignmentStateMachine does what SAMRecordAlignmentState should really do. It's correct in that it's more accurate than the LIB_position tests themselves. This is a non-broken, correct implementation. Needs cleanup, contracts, etc. -- This version is like 6x slower than the original implementation (according to the google caliper benchmark here). Obvious optimizations for future commit		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	HaplotypeCaller mode to skip assembly and genotyping for performance testing	2013-01-11 15:17:16 -05:00
public	Complete rewrite of low-level machinery of LIBS, not hooked up	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