[BioC] ShortRead QA

[Martin Morgan]

Steve Lianoglou <mailinglist.honeypot at gmail.com> writes:

> Hi Martin,
>
> On Fri, Jul 23, 2010 at 6:23 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> <snip>
>> It's total # of bases that'll be important, but if these are 'long'
>> reads then yes, likely memory is limiting (we're hoping  to take a
>> better approach to qa and other input functions over the next release,
>> though that doesn't help you at the moment).
>
> Are you at liberty to discuss what approaches you folks are
> considering? I'm curious. Is there some wiki page or something?

These are still being explored, with the main approaches a streaming /
block processing model or memory mapping. Streaming / block processing
seems more likely in the short term.

Our development plans are documented, in an internal-but-public way, at
http://wiki.fhcrc.org/bioc/DevPlans. Input welcome.

Martin

> Thanks,
> -steve

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793