Add dump subcommand and introduce reusable group filtering arguments

Introduces a new `dump` CLI command to export index k-mers as a CSV table. Adds a reusable `GroupFilterArgs` struct for ingroup/outgroup metadata-predicate quorum filtering with configurable count and fraction thresholds. Refactors the filter command to use explicit flags and a `GenomeSelector`-based pipeline, improving error handling and predicate application order. Exposes `IndexDump` from the `obikdump` crate and updates local dependencies accordingly.

This commit is contained in:

Eric Coissac

2026-08-26 14:33:45 +02:00

parent 737966899f

commit 768fa0183d

8 changed files with 165 additions and 78 deletions

src/Cargo.lock

Generated

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@@ -1667,6 +1667,7 @@ dependencies = [
  "csv",
  "obifastwrite",
  "obikalgorithm",
  "obikdump",
  "obikfilter",
  "obikindex",
  "obikindexer",