Project and/or aggregate the genome columns of an index into a new index. Where [`filter`](filter.md) selects rows (kmers), `select` operates on columns (genomes): grouping several genomes into one aggregated column, reordering columns, or dropping some.
`any`, `all`, `none` (logical, evaluated against `--presence-threshold`), `sum`, `min`, `max` (numeric, count index only). If a group's operator is left unspecified, it defaults to `any` when the source is a presence/absence index and `sum` when it stores counts.
A `select` never changes the underlying kmer set — only the per-genome data (counts or presence) is rewritten, so an unaggregated pass-through column (a plain genome label in `--select`) is a cheap copy.
At least one output column must be defined; every name listed in `--select` must resolve to either a defined group or an existing genome label. See [Genome predicates and taxonomy paths](predicates.md) for the predicate syntax used by `--group`.
## Disk usage
`select` always writes to a new output directory — there is no in-place mode. Each layer's kmer-identity files (MPHF, unitigs, evidence, fingerprint) never change under a column projection/aggregation, so they are hard-linked into the output rather than copied: no extra disk is used for them, even on a very large index. Linking falls back to a real copy automatically if it fails (e.g. `SOURCE`/`OUTPUT` on different filesystems). Use `--force-copy` to always copy instead — needed when the output must be able to survive independently of the source on disk (a hard link shares the same underlying data, so overwriting one path outside `select` itself would affect the other).
To replace an index with a selected version of itself, select to a temporary directory and swap it in:
