Is filter-abund objectively or subjectively slower than it used to be?
On Jul 5, 2013 11:55 PM, "C. Titus Brown" notifications@github.com wrote:

filter-abund seems really slow now! this would be good practice for making
normalize-by-median use the new thread stuff.

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On Fri, Jul 05, 2013 at 09:50:18PM -0700, mr-c wrote:

Is filter-abund objectively or subjectively slower than it used to be?

Same speed. Other things have sped up. Plus, it's using a Python-based
threading system, which I don't think is very efficient.

--titus

C. Titus Brown, ctb@msu.edu

Check out https://github.com/ctb/khmer/tree/be_threadwrite, especially line 59 onwards of filter-abund --

https://github.com/ctb/khmer/blob/be_threadwrite/scripts/filter-abund.py#L59

Comments?

Also see:

https://github.com/ctb/khmer/blob/be_threadwrite/scripts/normalize-by-median.py#L100

Not 100% working yet, but I think an unambiguous win in most ways.

See #92

See #1469, which simplifies the code instead :)