gatk3的最后一个经典版本3.8

Eric Banks 573ed07ad0 Fixed reported bug in BQSR for RNA seq alignments with Ns. ... * ClippingOp updated to incorporate Ns in the hard clips. * ReadUtils.getReadCoordinateForReferenceCoordinate() updated to account for Ns. * Added test that covers the BQSR case we saw. * Created GSA-856 (for Mauricio) to add lots of tests to ReadUtils. * It will require refactoring code and not in the scope of what I was willing to do to fix this.		2013-03-14 11:26:52 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	New GATKSAMRecord concept of a strandless read, update to FS	2013-03-13 11:16:36 -04:00
public	Fixed reported bug in BQSR for RNA seq alignments with Ns.	2013-03-14 11:26:52 -04:00
settings	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00