addpath('/mnt/biotheory/sethna/mouse_T/scripts/utils/');
addpath('/mnt/biotheory/sethna/mouse_T/scripts/TCR_Mus_2015/');

h = pwd;

cd '/mnt/biotheory/sethna/mouse_T/'


[genV, genD, genJ] = load_Mus_TCR_genomic_segments();
seq = repmat('A',1,150);

cd(h);

cfg = coder.config('mex');
cfg.DynamicMemoryAllocation = 'AllVariableSizeArrays';

h=pwd();

%cd scripts
model = Mus_V_DJ_cuts_insertions_dinuc_ntbias_model(genV, genD, genJ);
model.max_assignments = 5000;
model.call_codegen(genV, genD, genJ);

cd(h)
