All-vs-all PAF adapter

[cmdcolin]

This is an experimental stub for an "all vs all" PAF adapter. It is similar to the normal PAF adapter, except it assumes all refNames are prefixed with a assembly name

All-vs-all PAF can be produced by concatenating multiple genome assemblies into a single FASTA file, and running

minimap2 file.fa file.fa > out.paf

A command similar to the above is run by the PGGB workflow as a step (https://github.com/pangenome/pggb)

It is often advisable to include the assembly name in the FASTA file, so there is the PanSN spec that recommends prepending the assembly name (and haplotype number), example tool https://github.com/ekg/fastix

I ran this with about 14 different c.elegans assemblies and results look like this

Potentially this type of workflow can be leveraged to produce multi-way synteny visualizations in a more intuitive way. Instead of a user having to configure A vs B and B vs C manually, it is just known that all comparisons exist, so it can be automatically prepared.

Not all situations have all vs all, but for those that do, this can work

[cmdcolin]

Another example showing the all-vs-all PAF (top) versus the multi-sample VCF (bottom) of the same region

[cmdcolin]

There could be a need for a 'multi-lgv synteny display', this would put each alignment data in it's own 'row'