39 lines
1.6 KiB
Markdown
39 lines
1.6 KiB
Markdown
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# query
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Query an index with sequences and annotate each query with the kmer matches found.
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```bash
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obikmer query INDEX INPUTS... [OPTIONS]
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```
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## Arguments
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| Argument | Description |
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|---|---|
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| `INDEX` | Index directory to query against |
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| `INPUTS...` | Input sequence files (FASTA/FASTQ, gzip optional); at least one required |
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## Options
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| Option | Default | Description |
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|---|---|---|
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| `--detail` | off | Report per-position, per-genome coverage vectors in the output |
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| `--count-missing` | off | Also count query kmers absent from the index |
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| `--force-presence` | off | Report presence (0/1) per genome instead of raw counts |
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| `--presence-threshold` | `1` | Minimum accumulated count to declare a genome present (implies `--force-presence`) |
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| `-z, --findere-z` | derived from the index metadata | Override the Findere z parameter |
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| `-T, --threads` | detected core count | Number of worker threads |
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| `--chunk-size` | auto-sized (available RAM ÷ threads, clamped to 4–256 MiB) | I/O chunk size, in MiB |
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| `--max-open-files` | `threads / 4` (min 1) | Maximum number of input files open simultaneously |
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## Output
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FASTA on stdout, one record per query, annotated in the OBITools-style header format `>id {"key":value,...}`:
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- `kmer_count`: total number of kmers matched
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- `kmer_missing`: number of query kmers absent from the index (only with `--count-missing`)
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- `kmer_strict_matches`: per-genome match counts
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- `coverage`: per-position, per-genome coverage vectors (only with `--detail`)
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`--mismatch` is accepted by the CLI but not currently functional; using it produces a warning and is ignored.
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