feat: Implement query subcommand for sequence-to-genome mapping

This change introduces the `query` CLI command and its supporting infrastructure for sequence-to-genome mapping and k-mer matching. It adds a `QueryLayer` abstraction backed by MPHF and persistent matrices, exposes the index partition for direct querying, and implements `Hash`/`Eq` for `RoutableSuperKmer`. The command ingests sequence batches, deduplicates superkmers, routes them to index partitions for parallel exact or 1-mismatch matching, and outputs results as FASTA records annotated with JSON metadata. Includes `serde_json` dependency addition, module exports, and documentation updates.

This commit is contained in:

Eric Coissac

2026-05-21 13:23:05 +02:00

parent c8e591fc78

commit 13599dd444

13 changed files with 762 additions and 19 deletions

src/Cargo.lock

Generated

View File

@@ -1514,6 +1514,7 @@ dependencies = [
  "obisys",
  "pprof",
  "rayon",
  "serde_json",
  "speedytree",
  "tracing",
  "tracing-subscriber",