asivache 7c322780d3 Nway out fixed: in this mode a special nwayout sam writer is instantiated and passed to constrained manager. All the dispatching of the reads into separate output sam streams is taken care by that writer, so no other special processing is needed at the realigner/manager level. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6020 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-20 19:35:26 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Nway out fixed: in this mode a special nwayout sam writer is instantiated and passed to constrained manager. All the dispatching of the reads into separate output sam streams is taken care by that writer, so no other special processing is needed at the realigner/manager level.	2011-06-20 19:35:26 +00:00
test	Added stratification by discrete allele count, just like AF, but requiring genotypes so it can be exact. Added docs on wiki, and integrationtest using Kiran's very nice fundamental VCF	2011-06-19 03:11:00 +00:00