Add ability to list reference and haplotype paths

[adamnovak]

Changelog Entry

To be copied to the draft changelog by merger:

• vg paths now supports -H for selecting haplotype paths and -R for selecting reference paths

Description

When listing or removing paths with vg paths, we were able to ask for the generic paths, but not for other kinds of paths. Now we can ask for each of the three path types separately or in any combination. If none of the options are specified, we get all path types (the default).

[netwon123]

It is equal to the function 'vg convert -H' in v1.49?

[adamnovak]

I think the sense is reversed; vg convert -H is vg convert --drop-haplotypes, while vg paths -H is vg paths --haplotype-paths.

I think you can now use vg paths to get a graph without the haplotype paths in it, like vg convert -H, but you can also now use vg paths to e.g. get a list of the haplotype paths.

We might want to remove one of the two ways to do the same thing here?