sourmash

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specifying multiple lineages for `sourmash tax` commands

2

for sourmash `tax`, specify multiple taxonomy files like so: `sourmash tax annotate -g GATHER.csv --taxonomy DB_1.csv DB_2.csv` Here, `DB_1` and `DB_2` taxonomies will be loaded, with `DB_2` overwriting any shared...

bluegenes

tax in zip files; supporting multiple taxonomies with command-line switches

1

In https://github.com/sourmash-bio/sourmash/issues/2154, we've been talking about how to include taxonomic information in zipfiles, and I've been trying to figure out how that would work at the command line. But all...

ctb

check that reported `search` containment ani is using the right containment direction

6

for @ctb - If we're running `sourmash search`, are we producing the containment of the query in the reference, or the reference in the query? Thinking about it now I...

bluegenes

In https://github.com/sourmash-bio/sourmash/pull/2195, we added generic support for gzipped CSVs. In most of the codebase, we use `FileInputCSV` which will auto-detect gzipped files, but this is not yet usable by the...

ctb

add lineages/metadata summarization utility?

7

With #2211, I _think_ database preparation is going ok in one of the two scenarios, but we don't have a good `sourmash sig summarize`-style utility to take in a lineages...

bluegenes

`sourmash tax prepare` sometimes fails to create db?

1

I'm seeing some odd behavior, but not sure if this is server-related or sourmash related. On a compute node, `tax prepare` will refuse to prepare a new lineages database, saying...

bluegenes

Bump serde from 1.0.140 to 1.0.143

1

Bumps [serde](https://github.com/serde-rs/serde) from 1.0.140 to 1.0.143. Release notes Sourced from serde's releases. v1.0.143 Invert build.rs cfgs in serde_test to produce the most modern configuration in the default case (#2253, thanks...

dependabot[bot]

Bump memmap2 from 0.5.5 to 0.5.7

1

Bumps [memmap2](https://github.com/RazrFalcon/memmap2-rs) from 0.5.5 to 0.5.7. Changelog Sourced from memmap2's changelog. [0.5.7] - 2022-08-15 Changed Simplify file size retrieving code. @​saethlin [0.5.6] - 2022-08-11 Added Memory locking and unlocking. See...

dependabot[bot]

Bump primal-check from 0.3.1 to 0.3.2

1

Bumps [primal-check](https://github.com/huonw/primal) from 0.3.1 to 0.3.2. Commits ebd1ba9 Merge #43 1d8bf9f Add cargo-release config 2dfd5ca Update the CI lockfile 99050c6 Link licenses into sub-crates and bump releases 081d54d Merge #41...

dependabot[bot]

Bump pypa/cibuildwheel from 2.8.1 to 2.9.0

1

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.8.1 to 2.9.0. Release notes Sourced from pypa/cibuildwheel's releases. v2.9.0 🌟 CPython 3.11 wheels are now built by default - without the CIBW_PRERELEASE_PYTHONS flag. It's time to...

dependabot[bot]