gfatools-0.4 (r165)

Many changes since the last release:

• Revamped assembly graph cleaning. Now most cleaning operations are both
  count- and length-aware. Bubble popping become more precise. Also added
  topology-aware edge cutting that cuts weak edges while preserving the
  topological contiguity.

• Added the paf2gfa tool. It is essentially minisam combined with the new
  gfatools graph cleaning APIs. Currently it is specifically designed for PAFs
  generated by hifiasm.

• More meaningful graph linearization over inversions. The "blacklist" command
  now ignores inversions.

• Subgraph extraction now considers both directions to properly deal with
  starting segments in bubbles.

• Added the "bubble" command to output information of each bubble.

(23 December 2019, r165)