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feat: add select command for genome column projection and aggregation

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Introduces the `select` CLI command to project and aggregate genome-level k-mer data by column. Adds `filter` as an alias for `rebuild`. The implementation uses parallel partition processing, supports metadata-driven grouping with configurable aggregation operators, and performs atomic in-place rewrites or filtered exports. Updates documentation and navigation accordingly.
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Eric Coissac
2026-06-09 15:05:08 +02:00
parent b0dab452f6
commit e66adef23d
11 changed files with 958 additions and 1 deletions
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docmd/index.md
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| `superkmer` | Extract super-kmers from a sequence file and write to stdout |
| `index` | Build a complete genome index (scatter → dereplicate → count → layered MPHF) |
| `merge` | Merge multiple built indexes into one |
| `rebuild` | Filter and compact an existing index into a new single-layer index; supports the shared [kmer filtering](implementation/filtering.md) system |
| `rebuild` / `filter` | Filter and compact an existing index into a new single-layer index; supports the shared [kmer filtering](implementation/filtering.md) system (`filter` is an alias for `rebuild`) |
| `query` | Query an index with sequences and annotate matches |
| `dump` | Dump all indexed k-mers as CSV (kmer + per-genome counts or presence); supports the shared [kmer filtering](implementation/filtering.md) system; `--head N` limits output to the first N k-mers |
| `annotate` | Add or update genome metadata from a CSV file; or dump metadata as CSV |
| `distance` | Compute pairwise distance matrix between genomes; optionally build NJ/UPGMA trees; `--presence-threshold N` sets the minimum count to consider a k-mer present when computing Jaccard on count indexes (default 1) |
| `unitig` | Build a global de Bruijn graph across all partitions and enumerate its unitigs as FASTA; supports the shared [kmer filtering](implementation/filtering.md) system |
| `select` | Project and/or aggregate genome columns into a new or in-place index; the column-axis counterpart of `filter` (see [select](implementation/select.md)) |
| `estimate` | Estimate approximate-index parameters (z, evidence bits, FP rates) before indexing |
| `reindex` | Convert an index's evidence in-place: exact ↔ approx |
| `utils` | Miscellaneous index utilities: `--new-label NEW=OLD` renames a genome label; `--upgrade-index` adds missing `layer_meta.json` to old indexes |