#! /usr/bin/env julia


# Running SNaQ Analysis
using PhyloNetworks, SNaQ;
using Distributed;
addprocs(9);
@everywhere using PhyloNetworks, SNaQ;
nruns = 100; # number of runs for each hmax
astralfile = joinpath("..", "species_tree", "coal.tre");
astraltree = readnewick(astralfile);

inputCFfile = joinpath("..", "bucky", "bucky_1", "input.mb.CFs.csv");
inputCF = readtableCF(inputCFfile);
net0 = snaq!(astraltree, inputCF, hmax=0, filename="net0", seed=123, outgroup="ZJ", runs=nruns);
net1 = snaq!(net0, inputCF, hmax=1, filename="net1", seed=123, outgroup="ZJ", runs=nruns);
net2 = snaq!(net1, inputCF, hmax=2, filename="net2", seed=123, outgroup="ZJ", runs=nruns);
net3 = snaq!(net2, inputCF, hmax=3, filename="net3", seed=123, outgroup="ZJ", runs=nruns);
net4 = snaq!(net3, inputCF, hmax=4, filename="net4", seed=12345, outgroup="ZJ", runs=nruns);