v0.1.0: Initial release

Includes implementations of the following commands:

• align
• call (p-mutation, r-mutation)
• fdr (estimate, fix)
• spot (hot-features, cold-gaps)
• smooth (create, assemble)
• utils (gfa-to-fasta)

These are mostly derived from the ad hoc analysis code in the sheepgut repository. These commands are covered by a reasonably large set of tests, although some commands should ideally be better covered (there are a decent amount of uncovered lines in the align, fdr estimate, and fdr fix commands).

The planned commands to implement next are link (for constructing link graphs), matrix (for computing codon / amino acid mutation matrices), and covskew (for plotting coverage vs. skew, and computing peak-to-trough ratios).

This also includes some work-in-progress Jupyter notebooks demonstrating how to use strainFlye.

There isn't anything super special about this particular commit; I just wanted to tag a release as a starting point.