veg / hivclustering

Infer molecular transmission networks from pairwise distance files (part of HIV-TRACE)
2 stars 5 forks source link

Adding an interactive procedure to filtering triangles #11

Closed spond closed 8 years ago

spond commented 8 years ago

In networkbuild.py there is now simple iterative code which does this

  1. Consider up to N triangles (N is 2^16 by default, can be supplied as the -g argument on the command line)
  2. Filter all the N triangles, mark edges for removal. If no edges marked for removal, exit.
  3. Add N to the maximum number of triangles
  4. Consider up the current maximum number of triangles, but do not use the edges already marked in step 2.
  5. If tried this for more than 64 times, exit