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In https://github.com/dib-lab/sourmash/pull/1395, I detail some fun ways to make the rust code return invalid `MinHash` objects because `merge` does Bad Things when handed mixed pairs of abundance/non…
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#1808 adds support for SQLite, and is well enough tested (IMO :) that we could start fearlessly refactoring.
see blog post, http://ivory.idyll.org/blog/2022-storing-ulong-in-sqlite-sourmash.html, f…
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There are two refinements I'd like to explore with sourmash, which might improve on the current MinHash implementation.
1. Count vectors can be used to estimate overlap between sets with more effic…
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Dear sourmash-bio team,
this is a feature request.
Unlike nt-genomes I am comparing protein based minhashes.
Here, every single protein of one species and its corresponding minhash is compared to a…
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Hello, as of #2753 I have been able to build my own LCA databases from my existing sourmash signature databases.
I was interested in subsetting the current LCA database by taxonomy (i.e. Filtering …
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see https://github.com/dib-lab/sourmash/pull/856#issuecomment-578526048 - there,
ctb
> in `src/core/src/sketch/minhash.rs`, the `if ignore_abundance` code in `similarity` seems duplicative with t…
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on `latest`,
```
cd tests/test-data/
jq . < genome-s10+s11.sig > jq.sig
sourmash search genome-s10+s11.sig jq.sig -k 21 --dna
```
yields:
```
1 matches:
similarity match
---------- …
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Random gemisch / brainstorming about an opportunity I have to give a more in depth tech talk on sourmash at JGI in early May 2020. What should I cover?
An incomplete list of potential tech-y topics…
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Extending https://github.com/sourmash-bio/sourmash/issues/1750, I am copying a conversation between @ctb and @drtamermansour to be detailed later into tasks.
Slack Conversation
Tamer Mansour…
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see twitter thread https://twitter.com/amanjeev/status/1287422176711389184
Edit: we should also put "repeatable quests" in the issue tracker, e.g.
* update some few tests to use `@utils.in_tempdir…