feat: introduce genome metadata tracking and CSV export

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This commit replaces raw string genome labels with a structured `GenomeInfo` type for better metadata tracking. It adds a `--meta` flag to the index command, and implements a new `annotate` CLI subcommand to import metadata from CSV files or export it via `--dump`. Distance and shared-count matrices are now serialized to CSV, with UPGMA clustering trees exported as Newick files. Query outputs now include per-genome k-mer match counts in JSON, while fixing syntax and variable naming issues in index merging and dump generation.

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Eric Coissac

2026-05-22 09:28:58 +02:00

parent 77a0186fae

commit 0f8f61d3dd

14 changed files with 276 additions and 32 deletions

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