gatk3的最后一个经典版本3.8

Guillermo del Angel 3d49f524ee Small fixes for CalibrateGenotypeLikelihoods. ... -- If we are using an external vcf, do not consider filtered out records when argument -ignoreFiltered is set. -- Fix for R script: it uses ddply but some default R installations don't include plyr library by default.		2013-04-24 19:10:59 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Various bug fixes for recent Reduce Reads additions plus solution implemented for low MQ reads.	2013-04-24 18:18:50 -04:00
public	Various bug fixes for recent Reduce Reads additions plus solution implemented for low MQ reads.	2013-04-24 18:18:50 -04:00
settings	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Add additional necessary class files to na12878kb.jar target	2013-04-23 14:03:48 -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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00