`calyx_depth.py`: divest from odgi's Python bindings

[anshumanmohan]

The algorithm calls parse_data.py, which in turn calls odgi's Python bindings, to learn the input graph's dimensions. Instead, use mygfa.preprocess: https://github.com/cucapra/pollen/blob/de4f8dbee35003d2ce95d2df4b0300f56b4c0a54/mygfa/mygfa/preprocess.py#L64-L69

This will free us from odgi's Python bindings.

This work has been broken down as such:

• [x] #116
• [ ] #147
• [ ] https://github.com/cucapra/pollen/issues/148

For context, see tracking issue #105

[sampsyo]

Yay; this would be very satisfying!!