gatk3的最后一个经典版本3.8

Guillermo del Angel 49db96c8ad BAM pipeline fixes: a) temp workaround for DEV-9: -nWayOut argument in IndelRealigner is broken, for now things will only really work in single sample mode, b) correct extension of RealignerTargetCreator output, previous extension caused an error		2012-10-04 10:53:13 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Fixed ReduceReads bug where variant regions were missing.	2012-09-19 16:09:08 -04:00
public	First implementation of a generic 'bundled' Data Processing Pipeline for germline and cancer.	2012-09-25 17:13:50 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.gitignore	adding some directories to gitignore	2012-09-27 11:09:41 -04:00
build.xml	Convert external.build.dir and external.dist.dir back to paths	2012-08-15 23:04:10 -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	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00