26 lines
709 B
Markdown
26 lines
709 B
Markdown
|
# dump
|
||
|
|
|
||
|
|
Dump all kmers of an index as CSV, one row per kmer, with per-genome counts or presence.
|
||
|
|
|
||
|
|
```bash
|
||
|
|
obikmer dump INDEX [OPTIONS]
|
||
|
|
```
|
||
|
|
|
||
|
|
## Arguments
|
||
|
|
|
||
|
|
| Argument | Description |
|
||
|
|
|---|---|
|
||
|
|
| `INDEX` | Index directory to dump |
|
||
|
|
|
||
|
|
## Options
|
||
|
|
|
||
|
|
| Option | Default | Description |
|
||
|
|
|---|---|---|
|
||
|
|
| `--force-presence` | off | Output presence/absence (0/1) even if the index stores counts |
|
||
|
|
| `--debug` | off | Prefix each row with the partition and layer columns |
|
||
|
|
| `--head N` | none | Limit output to the first N kmers |
|
||
|
|
|
||
|
|
`dump` also accepts the shared [predicate options](filter.md#predicate-options) (`--ingroup`, `--outgroup`, `--min-count`, etc.) to restrict which kmers are dumped.
|
||
|
|
|
||
|
|
Output is CSV on stdout.
|