filter
Apply row-level selection to an index: retain only kmers matching ingroup/outgroup predicates over genome membership, plus optional total-count and complexity thresholds. The output is a new, single-layer index.
obikmer filter SOURCE -o OUTPUT [OPTIONS]
Arguments
| Argument | Description |
|---|---|
SOURCE |
Source index directory |
Options
| Option | Default | Description |
|---|---|---|
-o, --output |
— (required) | Output index directory |
-f, --force |
off | Overwrite an existing output directory |
--presence |
off | Output presence/absence instead of counts |
--min-total-count |
none | Minimum total count across all genomes (count index only) |
--max-total-count |
none | Maximum total count across all genomes |
--min-complexity |
none | Minimum normalized entropy (same score as --theta at index build time), recomputed from the stored unitig sequences |
--complexity-level-max |
6 |
Maximum sub-word size for the complexity score (used only with --min-complexity) |
Predicate options
| Option | Default | Description |
|---|---|---|
--ingroup |
none | Ingroup predicate (repeatable; each occurrence is ANDed) |
--outgroup |
none | Outgroup predicate (repeatable; each occurrence is ORed) |
--min-count |
0, or group size + N if negative | Minimum number of ingroup genomes carrying the kmer |
--max-count |
ingroup group size | Maximum number of ingroup genomes carrying the kmer |
--min-frac |
1.0 if --ingroup given without an explicit quorum, else 0.0 |
Minimum fraction of ingroup genomes |
--max-frac |
1.0 |
Maximum fraction of ingroup genomes |
--min-outgroup-count |
0 |
Minimum number of outgroup genomes carrying the kmer |
--max-outgroup-count |
0 if --outgroup given without an explicit quorum, else outgroup group size |
Maximum number of outgroup genomes |
--min-outgroup-frac |
0.0 |
Minimum fraction of outgroup genomes |
--max-outgroup-frac |
1.0 |
Maximum fraction of outgroup genomes |
--presence-threshold |
0 |
Minimum count for a genome to be considered a carrier of a kmer |
See Genome predicates and taxonomy paths for the predicate syntax used by --ingroup/--outgroup.
A negative --min-count/--max-count is interpreted as an offset from the group size — e.g. --min-count=-1 means "all but one".
Declaring --ingroup with no explicit ingroup quorum flag implicitly sets --min-frac 1.0 (present in every ingroup genome). Declaring --outgroup with no explicit outgroup quorum flag implicitly sets --max-outgroup-count 0 (absent from every outgroup genome). Any explicit quorum flag for a group disables that group's implicit default.