Generate a partial order alignment

[urbanslug]

Is your feature request related to a problem? Please describe

If we can perform partial order alignment on reads and generate a variation graph. I don't know of another tool that does this. It would carve out a niche for graphite.

Describe the solution you'd like

Implement a partial order alignment in racket that graphite can use

Describe alternatives you've considered

Use the racket C API and libraries:

• https://github.com/vgteam/gssw
• https://github.com/rvaser/spoa

Additional context

---

Implementation plan

• String to graph alignment
• Topological sort
• Insertion of aligned sequence

References

• Understanding Partial Order Alignment for Multiple Sequence Alignment
• Striped Smith–Waterman speeds database searches six times over other SIMD implementations
• Multiple sequence alignment using partial order graphs