gatk3的最后一个经典版本3.8

Mark DePristo 7ae15dadbe HC now by default only uses reads with MAPQ >= 20 for assembly and calling ... -- Previously we tried to include lots of these low mapping quality reads in the assembly and calling, but we effectively were just filtering them out anyway while generating an enormous amount of computational expense to handle them, as well as much larger memory requirements. The new version simply uses a read filter to remove them upfront. This causes no major problems -- at least, none that don't have other underlying causes -- compared to 10-11mb of the KB -- Update MD5s to reflect changes due to no longer including mmq < 20 by default		2013-03-21 13:10:50 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	HC now by default only uses reads with MAPQ >= 20 for assembly and calling	2013-03-21 13:10:50 -04:00
public	HC now by default only uses reads with MAPQ >= 20 for assembly and calling	2013-03-21 13:10:50 -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