the bubbles

[ekg]

Path-based bubble finding.

Goals:

1. fast bubble finding in complex graphs (linear/banded in reference length)
2. reference-based bubble finding
3. non-canonical bubble finding to resolve "snarl insensitivity" issue where the first variable site within a bubble is ignored
4. untangling approach used in vg deconstruct to ground coordinates and filter out ambiguous or conflicting observations, and possible integration of odgi untangle grounding
5. VCF output from odgi bubble
6. bubble chain finding