PanBreak 0.2.0

Added

• panbreak graph --builder minigraph: locus graphs built natively with minigraph (-cxggs), with
  assembly paths from minigraph -cxasm --vc; runs on macOS without containers.
• panbreak graph --builder cactus: locus graphs built with Minigraph-Cactus (cactus-pangenome) in a
  digest-pinned container or a native install.
• panbreak convert: imports GFA with P lines, W lines (Minigraph-Cactus, vg) or minigraph rGFA
  with GAF alignments, and extracts a locus from a large graph with odgi (--region).
• --skip-build (alias of --skip-pggb) reuses the output of any builder.
• panbreak check lists minigraph and cactus-pangenome and the available graph builders.

Changed

• bubbles reverses paths that run against the reference orientation.
• bubbles ignores path events within --cover-pad bp of a path end (unanchored sequence ends);
  results on pggb graphs of the example are unchanged.
• --trim-up/--trim-down match paths by sample name, so they work with any builder.
• minigraph is part of the conda environment.

On the synthetic example the three builders give highly consistent results: genotype concordance 99.89 % (pggb), 99.87 % (minigraph) and 99.88 % (Minigraph-Cactus), with 100 % carrier sensitivity and no false carriers. These are preliminary results on toy data; reports from real loci are very welcome as GitHub issues.