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.
(21 March 2021, r234)
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)
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)
Support SR tags on L-lines.
(7 August 2019, r51)
Initial release.
(6 July 2019, r40)