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sourmash-bio / sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.
http://sourmash.readthedocs.io/en/latest/
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Why must scale be >=100? #2064

Closed dkoslicki closed 2 years ago

dkoslicki commented 2 years ago

I've noticed that sourmash requires the scale to be >= 100, but at times (especially for testing purposes) it would be handy to set a scaled=1. Is there a technical limitation or other rational of why the scale can't be any smaller than 100?

ctb commented 2 years ago

it's a warning - it's not enforced in any way. We use scaled=1 all the time :).

ctb commented 2 years ago

(it's just really, really slow; we don't want users new to the FracMinHash concept to settle on it and then complain "but it's really slow (when we use it in this off label way!)"

dkoslicki commented 2 years ago

Ah, gotcha. I misinterpreted the warning as it changing 1 to 100.