Simulate loop extrusion by loop extruding factors and analyse the resulting structures of loops.

• simlef.pyx - simulate loop extrusion in 1d with simulate()

• looptools.py - analyse the structure of extruded loops:

  • build trees of nested loops with get_parent_loops()
  • find root loops with get_roots()
  • identify the positions between the root loops with get_backbone()
  • identify stacked LEFs with stack_lefs()

• loopviz.py - visualize loops with plot_lefs()

• simlef_twosided.pyx - simulate loops extrusion with synchronized extrusion blocking