Allow user to specify root sequence

[zmertens]

• [ ] Added three new do functions to dawg::root_model
  • [ ] do_user_seq
  • [ ] do_user_rates
  • [ ] do_user_seq_rates

• [ ] Modify dawg::root_model::create to select the do functions based on whether rates or seq are empty

[zmertens]

How does Dawg currently handle the root sequence? I thought it might be mocked in 'matic.cpp' but could not find it.

[reedacartwright]

Each matic_section has a root_model rut_mod member variable.

https://github.com/reedacartwright/dawg/blob/9c44bdc8cb1ebbfca4cddf4976841d734cf09288/src/include/dawg/matic.h#L53

https://github.com/reedacartwright/dawg/blob/9c44bdc8cb1ebbfca4cddf4976841d734cf09288/src/lib/matic.cpp#L65

[zmertens]

Where are the root sequence and rates used? Are they part of the sequence structure?

[reedacartwright]

Each residue in a sequence has a base and a rate associated with it. do_stat generates these from a model: https://github.com/reedacartwright/dawg/blob/9c44bdc8cb1ebbfca4cddf4976841d734cf09288/src/include/dawg/root.h#L41-L42

The other do_ functions will need to either generate them from a model or use the values specified by the user.

[zmertens]

The other do_ functions will need to either generate them from a model or use the values specified by the user.

Oh, that's straightforward. I saw the rate_cat but I confused base and root_seq.

[reedacartwright]

Fixed in #36