obikmer/UserDocMD/usage/select.md

select

Project and/or aggregate the genome columns of an index into a new (or in-place) index. Where filter selects rows (kmers), select operates on columns (genomes): grouping several genomes into one aggregated column, reordering columns, or dropping some.

obikmer select SOURCE (--output OUTPUT | --in-place) [OPTIONS]

Arguments

Argument	Description
SOURCE	Source index directory

Options

Option	Default	Description
--output	—	Output index directory (mutually exclusive with --in-place)
--in-place	off	Rewrite the source index in place (mutually exclusive with --output)
-f, --force	off	Overwrite an existing output directory
--group NAME:PRED	none	Define a named group of genomes by predicate (repeatable; mutually exclusive with --aggregate-by)
--group-op NAME:OP	none	Aggregation operator for a named group
--aggregate-by KEY	none	Automatically create one group per distinct value of a metadata key (mutually exclusive with --group)
--aggregate-op OP	none	Aggregation operator applied to every auto-generated group
--select COL,...	all columns	Output columns, in order (group names or genome labels)
--presence-threshold	0	Minimum count for a genome to be considered a carrier (logical operators only)

Aggregation operators

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 of --output/--in-place is required, and 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 for the predicate syntax used by --group.