merge
Merge multiple built indexes into a single index.
obikmer merge -o OUTPUT SOURCE... [OPTIONS]
Arguments
| Argument | Description |
|---|---|
SOURCE... |
Index directories to merge (at least one required) |
Options
| Option | Default | Description |
|---|---|---|
-o, --output |
— (required) | Output index directory |
--force |
off | Overwrite an existing output directory |
--force-presence |
off | Store the merged index as presence/absence even if all sources have counts |
--rename-duplicates |
off | Disambiguate duplicate genome labels (.1, .2, …) instead of failing |
--budget-fraction |
0.5 |
Fraction of available RAM reserved as the memory budget for parallel partition merging |
Behaviour
The output mode is chosen automatically: if every source index stores counts, the merged index stores counts too; otherwise it is presence/absence. --force-presence forces presence/absence regardless of the sources.
By default, merging two indexes that share a genome label fails with an error; --rename-duplicates instead appends a numeric suffix to keep both copies.