gatk3的最后一个经典版本3.8

Mark DePristo 38cc496de8 Move SomaticIndelDetector and associated tools and libraries into private/andrey package ... -- Intermediate commit on the way to archiving SomaticIndelDetector and other tools. -- SomaticIndelDetector, PairMaker and RemapAlignments tools have been refactored into the private andrey package. All utility classes refactored into here as well. At this point, the SomaticIndelDetector builds in this version of the GATK. -- Subsequent commit will put this code into the archive so it no longer builds in the GATK		2012-12-29 14:34:08 -05:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	Protect against non-standard ref bases. Ryan, please review.	2012-12-26 15:46:21 -05:00
public	Move SomaticIndelDetector and associated tools and libraries into private/andrey package	2012-12-29 14:34:08 -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	Clover report excludes test files and other non-interesting files from the clover reports	2012-12-29 13:31:07 -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	Use build jars in test classpaths by default	2012-11-28 22:57:04 -05:00