Polish
Description
Realigns blocks of a multiple sequence alignment pangraph with an external multiple sequence alignment tool. Requires MAFFT command to be available in PATH.
Options
| Name | Type | Short Flag | Long Flag | Description |
|---|---|---|---|---|
| Maximum Length | Integer | l | length | cutoff above which the block is not realigned externally |
| Preserve Case | Bool | c | preserve-case | ensure case (upper/lower) is preserved after realignment |
Arguments
Zero or one pangraph file which must be formatted as a JSON. If no file path is given, reads from stdin. In either case, the stream can be optionally gzipped.
Output
Outputs the polished pangraph to stdout.