asivache 43812a28fc If among all the multiple alignments for the given read we have 'unmapped' ones (can happen with bwa 0.5.7 and maybe later versions), then discard the latters and keep only the mapped ones. Keep 'unmapped' only if its the only alignment available. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5090 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-26 20:07:08 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	If among all the multiple alignments for the given read we have 'unmapped' ones (can happen with bwa 0.5.7 and maybe later versions), then discard the latters and keep only the mapped ones. Keep 'unmapped' only if its the only alignment available.	2011-01-26 20:07:08 +00:00
test	added integration test for --sites_only option	2011-01-26 14:58:15 +00:00