gfatools-0.5 (r234)

Many changes:

• Use Tarjan's SCC algorithm to identify bubble. This algorithm is more robust
  to inversions, but requires reference paths.

• Generate unitig sequences from assembly graphs.

• Use BFS to extract subgraphs within a radius. The older code uses DFS which
  is sometimes counter-intuitive.

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)

gfatools-0.3 (r70)

Notable changes:

• Generate blacklisted regions from rGFA. The current implementation assumes a
  minigraph graph. It is not general.

• Output basic statistics of GFA graphs.

• Check and remove multiple edges.

(22 August 2019, r70)

gfatools-0.2 (r51)

Support SR tags on L-lines.

(7 August 2019, r51)

gfatools-0.1 (r40)

Initial release.