gatk3的最后一个经典版本3.8

Mark DePristo 965043472a Vastly more powerful, cleaner graph simplification approach ... -- Generalizes previous node merging and splitting approaches. Can split common prefixes and suffices among nodes, build a subgraph representing this new structure, and incorporate it into the original graph. Introduces the concept of edges with 0 multiplicity (for purely structural reasons) as well as vertices with no sequence (again, for structural reasons). Fully UnitTested. These new algorithms can now really simplify diamond configurations as well as ones sources and sinks that arrive / depart linearly at a common single root node. -- This new suite of algorithms is fully integrated into the HC, replacing previous approaches -- SeqGraph transformations are applied iteratively (zipping, splitting, merging) until no operations can be performed on the graph. This further simplifies the graphs, as splitting nodes may enable other merging / zip operations to go.		2013-03-23 17:40:55 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Vastly more powerful, cleaner graph simplification approach	2013-03-23 17:40:55 -04:00
public	Added support to reduce reads to Callable Loci	2013-03-21 15:53:04 -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