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simlef.pyx - simulate loop extrusion in 1d with simulate()
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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()
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loopviz.py - visualize loops with plot_lefs()
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simlef_twosided.pyx - simulate loops extrusion with synchronized extrusion blocking