gatk3的最后一个经典版本3.8

Eric Banks b07bf1950b Adding an integration test for another feature that I snuck in during a previous commit: we now allow lower-case bases in the REF/ALT alleles of a VCF and upper-case them (this had been turned off because the previous version used Strings to do the uppercasing whereas we stick with byte operations now).		2012-07-29 22:19:49 -04:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	Final checkpoint: all tests pass. Note that there were bugs in the PoolGenotypeLikelihoodsUnitTest that needed fixing and eventually led to my needing to disable one of the tests (with a note for Guillermo to look into it). Also note that while I have moved over the GATK to use the new non-null representation of Alleles, I didn't remove all of the now-superfluous code throughout to do padding checking on merges; we'll need to do this on a subsequent push.	2012-07-29 01:07:59 -04:00
public	Adding an integration test for another feature that I snuck in during a previous commit: we now allow lower-case bases in the REF/ALT alleles of a VCF and upper-case them (this had been turned off because the previous version used Strings to do the uppercasing whereas we stick with byte operations now).	2012-07-29 22:19:49 -04:00
settings	Removed Categories.	2012-07-25 13:46:24 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	Remove reference dependence in BCF2Codec	2012-07-25 08:56:38 -04:00
ivy.xml	Added the ability to update the Forum	2012-07-23 17:17:33 -04:00