gatk3的最后一个经典版本3.8

Mauricio Carneiro 2c0bf89961 Co-Reduction implementation in ReduceReads ... ReduceReads now co-reduces bams if they're passed in toghether with multiple -I. Co-reduction forces every variant region in one sample to be a variant region in all samples. Also: * Added integrationtest for co-reduction * Fixed bug with new no-recalculation implementation of the marksites object where the last object wasn't being removed after finalizing a variant region (updated MD5's accordingly) DEV-200 #resolve #time 8m		2012-11-06 13:49:07 -05:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	Co-Reduction implementation in ReduceReads	2012-11-06 13:49:07 -05:00
public	Co-Reduction implementation in ReduceReads	2012-11-06 13:49:07 -05:00
settings	Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component.	2012-10-16 02:22:30 -04:00
.gitignore	adding some directories to gitignore	2012-09-27 11:09:41 -04:00
build.xml	Added mvninstall.queue.all target which includes private, along with supporting sub-targets.	2012-10-31 11:49:50 -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	Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component.	2012-10-16 02:22:30 -04:00