wwood
commented
9 years ago Hey on the face of it this looks great, but I'm super busy at the moment. I'll merge soon, just wanted to make sure you weren't feeling under-appreciated.
On 6 March 2015 at 00:08, timbalam notifications@github.com wrote:
Improvements to bubble algorithm.
Bubbles with cyclic paths are allowed. If a path with a cycle is found, it is added to bubble known problems and not to queue, preventing it from being re-yielded. Once a bubble converges, the each_path method will yield paths that contain less than a specified number of cycles (but never a cycle through the converged node).
Algorithm forbids cycles in linear mode, and allows bubble cycles through
previously seen path nodes.
You can view, comment on, or merge this pull request online at:
https://github.com/wwood/finishm/pull/26 Commit Summary
- Minor edits.
- Started to add circuit resolution.
- Fixed a couple of bugs.
- Added new bubble test. Gets weird error,
- Added new bubble test. Gets weird error,
- Fixed weird error. New test breaks bubble algorithm.
- Implemented new convergence algorithm. each_path returns duplicate paths. Attempted fix failed.
- Found error in new convergence algorithm.
- New algorithm passes more tests, so is correct!!!
- each path now should yield all paths once. bubble shorthand returns bubble path shorthands in sorted order instead of yield order.
- Start to add cycles.
- Fixing some issues with reference trails.
- Use reference trail priority for yielding paths using each_path.
- Updated circuit tests to reflect circular paths can be resolved.
File Changes
- M ext/src https://github.com/wwood/finishm/pull/26/files#diff-0 (2)
- M lib/assembly/bubbly_assembler.rb https://github.com/wwood/finishm/pull/26/files#diff-1 (479)
- M lib/assembly/single_coherent_paths_between_nodes.rb https://github.com/wwood/finishm/pull/26/files#diff-2 (32)
- M lib/assembly/single_ended_assembler.rb https://github.com/wwood/finishm/pull/26/files#diff-3 (6)
- M spec/bubbly_assembler_spec.rb https://github.com/wwood/finishm/pull/26/files#diff-4 (158)
Patch Links:
— Reply to this email directly or view it on GitHub https://github.com/wwood/finishm/pull/26.
Ben Woodcroft http://ecogenomic.org/users/ben-woodcroft http://www.ecogenomic.org/
timbalam
Improvements to bubble algorithm.
Bubbles with cyclic paths are allowed. If a path with a cycle is found, it is added to bubble known problems and not to queue, preventing it from being re-yielded. Once a bubble converges, the each_path method will yield paths that contain less than a specified number of cycles (but never a cycle through the converged node).
Algorithm forbids cycles in linear mode, and allows bubble cycles through previously seen path nodes.