Minimize the minimal `pggb` command line

pangenome / pggb

the pangenome graph builder

https://doi.org/10.1038/s41592-024-02430-3

MIT License

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Minimize the minimal `pggb` command line #346

Closed AndreaGuarracino closed 11 months ago

AndreaGuarracino commented 11 months ago

PanSN is required in vg. Now, pggb requires PanSN by default, but this can be deactivated with --no-pansn. With PanSN, we can compute the number of haplotypes automatically, leading to the minimal command line

pggb -i seq.fa

ekg commented 11 months ago

Why not require -n when we don't have pansn but otherwise allow it to be dropped?

On Wed, Oct 25, 2023, 19:05 Andrea Guarracino @.***> wrote:

Merged #346 https://github.com/pangenome/pggb/pull/346 into master.

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