seq = repmat('A',1,150);

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

h = pwd;
cd('/mnt/biotheory/sethna/mouse_T/scripts/utils/')
codegen align_with_constraints_fast_left -config cfg -o align_with_constraints_fast_left -args {coder.typeof(seq,[1 inf]), coder.typeof(seq,[1 inf]), 10,  3, coder.typeof(zeros(10,1),[inf 1]) }
codegen align_with_constraints_fixed_left -config cfg -o align_with_constraints_fixed_left -args { coder.typeof(seq,[1 inf]), coder.typeof(seq,[1 inf]), 10, 3}
cd(h)

%clear model
%model = V_DJ_cuts_insertions_dinuc_ntbias_model(genV, genD, genJ);
%model.max_assignments = 5000;
%model.call_codegen(genV, genD, genJ);




