asivache 6dd41c8489 Nway writer takes another argument: whether to create index on the fly. Realigner in NWayOut mode currently will ALWAYS create index on the fly as there seems to be no clean way to extract the requested value from argument collection in the presence of a different @Output stream. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6023 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-21 17:26:04 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Nway writer takes another argument: whether to create index on the fly. Realigner in NWayOut mode currently will ALWAYS create index on the fly as there seems to be no clean way to extract the requested value from argument collection in the presence of a different @Output stream.	2011-06-21 17:26:04 +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