Marginalize
Description
Compute all pairwise marginalizations of a multiple sequence alignment pangraph.
Options
| Name | Type | Short Flag | Long Flag | Description |
|---|---|---|---|---|
| Output path | String | o | output-path | Path to direcotry where the output of all pairwise mariginalizations will be stored if supplied |
| Reduce paralogs | Boolean | r | reduce-paralog | Collapses coparallel paths through duplicated blocks. |
| Projection strains | String | s | Strains | Collapses the graph structure to only blocks and edges contained by the paths of the supplied strain names. comma seperated, no spaces |
| Consistency check | Boolean | t | test | toggle to activate consistency check: verifies that output genomes are exactly equal to input genomes |
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 all pairwise graphs to the directory at the user-supplied path.