1.0.1 test

[kyzhu]

Main changes:

1. For each individual steps, added subcommand so no need to call *.py
2. If input is *.hic, try to remove the intermediate *.cool output from hic2cool
3. Make matrix expansion default after the reconstruct (used to be spatial_structure.py) option
4. Make thread limitation with threadpool_limits non-default
5. Removed objective_value.py

[kyzhu]

@Eric0627 I did not change the solution to the one with the best objective, because in most (>95%) runs, the final iteration gives the best objective.