gatk3的最后一个经典版本3.8

Mark DePristo f42bb86bdd e# This is a combination of 2 commits. ... Only try to clip adaptors when both reads of the pair are on opposite strands -- Read pairs that have unusual alignments, such as two reads both oriented like: <----- <----- where previously having their adaptors clipped as though the standard calculation of the insert size was meaningful, which it is not for such oddly oriented pairs. This caused us to clip extra good bases from reads. -- Update MD5s due change in adaptor clipping, which add some coverage in some places		2013-05-03 11:19:14 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	e# This is a combination of 2 commits.	2013-05-03 11:19:14 -04:00
public	e# This is a combination of 2 commits.	2013-05-03 11:19:14 -04:00
settings	Rev'd up Picard to get PL fix: PLs were saturated to 32767 (Short.MAX_VALUE) when converting from GL to integers. Increase capping to Integer.MAX_VALUE (2^31-1) which should be enough for reasonable sites now. Integration tests change because some tests have some hyper-deep pileups where this case was hit	2013-05-02 16:31:43 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
build.xml	Include cofoja jar in classpath when testing release jars	2013-04-30 22:16:58 -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