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bluegenes / thumper

Thumper: One of the types of stills used to accomplish the second distillation of American whiskey. It effectively removes impurities and concentrates the alcohol even further. “Low wines” go in; “high wines” come out. Thumpers differ from doublers in that the low wines enter a thumper as vapors that are bubbled through water, causing the stills to make a thumping sound; a doubler makes no distinctive noise since the low wines enter in condensed, liquid form.
https://bluegenes.github.io/thumper/
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switch method for ignoring exact db matches #15

Closed bluegenes closed 3 years ago

bluegenes commented 3 years ago

ref dib-lab/sourmash#433

dib-lab/sourmash#1477 added underlying support for this (see JaccardSearch variant https://github.com/dib-lab/sourmash/blob/latest/tests/test_index.py#L1202-L1219).

A test shows how to set the search_fn:

...now search with something that should ignore sig47, the exact match. search_fn = JaccardSearchBestOnly_ButIgnore([ss47])

100% matches are currently ignored during gather taxonomic summarization, but switching to ignoring them during prefetch would enable direct gather-csv --> taxonomic summarization?

bluegenes commented 3 years ago

Enabled this with exclusionary picklists in https://github.com/sourmash-bio/sourmash/pull/1623