gatk3的最后一个经典版本3.8

Mark A. DePristo 527fbeaf3c Extensive unit tests for DiffNodes, Diffelements, and DiffLeafs data structure. The lack of unity in these three data structures is a bit gross, to be honest, but it might may not be a significant factor when I reach implementing the generic diff functions. The problem is that ideally these would look like the scheme structures: ... (A B (C D E)) which is a nested list containing A and B items and a sublist of C D E. Here there are only two classes: lists and everything else. Right now we have three. DiffNodes, which contain both atomic fields (A B) as well as the subnodes ((C D E)) here. These a specific class for DiffLeaf, which is really just a pair mapping name=value. And DiffElement contains a named item, since all objected in the hierarchy have a name. It's just doesn't feel right to me right now. Ultimately the problem is that you want the objects to be self-describing, so the DiffElement and DiffLeaf are a clean factoring the need for names in both the values and the nodes.		2011-07-04 19:34:15 -04:00
public	First working version of the DiffNode readers for VCF and BAM files. Unit tests confirm the readers are approximately working. Skeleton of a working DiffObjects walker that will be able to provide detailed information about how exactly two files of the same type differ, so long as the files are supported by the DiffNode structure.	2011-07-04 16:11:42 -04:00
settings	Updated the tribble jar -- this should fix most of the integration test	2011-06-29 01:11:03 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	Fixes to the packaging system to work with the new directory structure.	2011-06-30 18:27:17 -04:00
ivy.xml	A prototype script and library dependencies to extract a BAM list from a	2011-06-22 22:53:45 +00:00