GFA space output for vg snarls

[adamnovak]

Changelog Entry

To be copied to the draft changelog by merger:

• vg autoindex supports --gbwt-buffer-size to increase the buffer size for indexing long haplotypes.
• vg snarls now supports --named-coordinates for reporting snarls and snarl traversals in input GFA coordinates.

Description

This adds the --named-coordinates option to vg snarls, so you can get snarls on a GFA file or GBZ graph and get your output in terms of GFA space. I had to add a new name member on the Visit to support this.

I'm also dong a little hacky rewriting of traversals, to elide the multiple visits to trivial snarls and different fragments of a segment that you get when a segment is split. The result of this is that if the traversal finder reports cyclic traversals that loop around on a node, the looping will be elided. I probably want to fix that.

[adamnovak]

Here's a static binary of this: https://ipfs.io/ipfs/QmQH3C1GUUVekLDMYfXwESLFUL3sJU3JrJXN8gVkHv78jD