Making RQC generator output compatible with qFlex input.

[s-mandra]

[s-mandra]

See #101.

[alexandrupaler]

Is this still an issue?

[s-mandra]

It is still an issue. I have few workaround that could be potentially implemented, but it would be better if the rqc generator would output the circuit using the same indexes for qubits that qflex actually uses.