gatk3的最后一个经典版本3.8

Mark DePristo f5a301fb63 Bugfix for AlignmentUtils.trimCigarByBases ... -- Previous version would trim down 2M2D2M into 2M if you asked for the first 2 bases, but this can result in incorrect alignment of the bases to the reference as the bases no longer span the full reference interval expected. Fixed and added unit tests		2013-05-03 09:32:05 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	leftAlignCigarSequentially now supports haplotypes with insertions and deletions where the deletion allele was previously removed by the leftAlignSingleIndel during it's cleanup phase.	2013-05-03 09:32:05 -04:00
public	Bugfix for AlignmentUtils.trimCigarByBases	2013-05-03 09:32:05 -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