48 lines
2.7 KiB
Markdown
48 lines
2.7 KiB
Markdown
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# filter
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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.
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```bash
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obikmer filter SOURCE -o OUTPUT [OPTIONS]
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```
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## Arguments
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| Argument | Description |
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|---|---|
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| `SOURCE` | Source index directory |
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## Options
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| Option | Default | Description |
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|---|---|---|
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| `-o, --output` | — (required) | Output index directory |
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| `-f, --force` | off | Overwrite an existing output directory |
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| `--presence` | off | Output presence/absence instead of counts |
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| `--min-total-count` | none | Minimum total count across all genomes (count index only) |
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| `--max-total-count` | none | Maximum total count across all genomes |
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| `--min-complexity` | none | Minimum normalized entropy (same score as `--theta` at index build time), recomputed from the stored unitig sequences |
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| `--complexity-level-max` | `6` | Maximum sub-word size for the complexity score (used only with `--min-complexity`) |
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## Predicate options
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| Option | Default | Description |
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|---|---|---|
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| `--ingroup` | none | Ingroup predicate (repeatable; each occurrence is ANDed) |
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| `--outgroup` | none | Outgroup predicate (repeatable; each occurrence is ORed) |
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| `--min-count` | 0, or group size + N if negative | Minimum number of ingroup genomes carrying the kmer |
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| `--max-count` | ingroup group size | Maximum number of ingroup genomes carrying the kmer |
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| `--min-frac` | `1.0` if `--ingroup` given without an explicit quorum, else `0.0` | Minimum fraction of ingroup genomes |
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| `--max-frac` | `1.0` | Maximum fraction of ingroup genomes |
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| `--min-outgroup-count` | `0` | Minimum number of outgroup genomes carrying the kmer |
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| `--max-outgroup-count` | `0` if `--outgroup` given without an explicit quorum, else outgroup group size | Maximum number of outgroup genomes |
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| `--min-outgroup-frac` | `0.0` | Minimum fraction of outgroup genomes |
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| `--max-outgroup-frac` | `1.0` | Maximum fraction of outgroup genomes |
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| `--presence-threshold` | `0` | Minimum count for a genome to be considered a carrier of a kmer |
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See [Genome predicates and taxonomy paths](predicates.md) for the predicate syntax used by `--ingroup`/`--outgroup`.
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A negative `--min-count`/`--max-count` is interpreted as an offset from the group size — e.g. `--min-count=-1` means "all but one".
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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.
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