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update search documentation to make it clear what "query" and "subject" are #3543

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ctb opened this issue Feb 23, 2025 · 0 comments
Open

update search documentation to make it clear what "query" and "subject" are #3543

ctb opened this issue Feb 23, 2025 · 0 comments

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@ctb
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ctb commented Feb 23, 2025

back when (#2968) we updated the docs for search --containment and prefetch to make it clear that the arguments were swapped - search --containment genome metagenomes... vs prefetch metagenome genomes...

We should add more/better docs for:

  • gather - metagenome x genomes
  • manysearch - genomes x metagenomes
  • fastmultigather - metagenomes x genomes
  • multisearch - genomes x genomes

and maybe others
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