Closed zmertens closed 6 years ago
How does Dawg currently handle the root sequence? I thought it might be mocked in 'matic.cpp' but could not find it.
Each matic_section
has a root_model rut_mod
member variable.
Where are the root sequence and rates used? Are they part of the sequence
structure?
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.
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
.
Fixed in #36
do
functions todawg::root_model
do_user_seq
do_user_rates
do_user_seq_rates
dawg::root_model::create
to select the do functions based on whether rates or seq are empty