function (i)readIntTable(s$ path)
{
	if (!fileExists(path))
	stop("readIntTable(): File not found at path " + path);
	l = readFile(path);
	m = sapply(l, "asInteger(strsplit(applyValue));", simplify="matrix");
	return t(m);
}
initialize() {
initializeSLiMModelType("nonWF");
initializeSLiMOptions(nucleotideBased=T);
length = initializeAncestralNucleotides("/mnt/rstor/SOM_EPBI_FRS2/zxc307/1000g2021/fasta/hs37d5_chr22.fa");
defineConstant("L", length);
defineConstant("K", 200);
initializeMutationTypeNuc("m1", 0.5, "f", 0.0);
m1.convertToSubstitution = T;
initializeGenomicElementType("g1", m1, 1.0, mmJukesCantor(1e-7));
initializeGenomicElement(g1, 0, L-1); 
initializeRecombinationRate(1e-8);
// read in the pedigree log files
defineConstant("M", readIntTable("mating.txt"));
defineConstant("D", readIntTable("death.txt"));
// extract the ticks for quick lookup
defineConstant("Mt", drop(M[,0]));
defineConstant("Dt", drop(D[,0]));
}
reproduction() {
// generate all offspring for the tick
m = M[Mt == community.tick,];
for (index in seqLen(nrow(m))) {
row = m[index,];
ind = subpop.subsetIndividuals(tag=row[,1]);
mate = subpop.subsetIndividuals(tag=row[,2]);
child = subpop.addCrossed(ind, mate);
child.tag = row[,3];
}
self.active = 0;
}
1 early() {
sim.addSubpop("p1", 90);
// provide initial tags matching the original model
p1.individuals.tag = 1:90;
}
early() {
// execute the predetermined mortality
inds = p1.individuals;
inds.fitnessScaling = 1.0;
d = drop(D[Dt == community.tick, 1]);
indices = match(d, inds.tag);
inds[indices].fitnessScaling = 0.0;
}
1 late() {
	p1.genomes.readFromVCF("/mnt/rstor/SOM_EPBI_FRS2/zxc307/1000g2021/GBR/GBR.chr22.90.recode.vcf", m1);
log = sim.createLogFile("./test.log",logInterval=1);
	log.addGeneration();
	log.addSubpopulationSize(p1);
	log.addCustomColumn("FreqA", "nucleotideFrequencies(sim.chromosome.ancestralNucleotides())[0];");
	log.addCustomColumn("FreqC", "nucleotideFrequencies(sim.chromosome.ancestralNucleotides())[1];");
	log.addCustomColumn("FreqG", "nucleotideFrequencies(sim.chromosome.ancestralNucleotides())[2];");
	log.addCustomColumn("FreqT", "nucleotideFrequencies(sim.chromosome.ancestralNucleotides())[3];");
} 
1:5 late() {
	mut = sim.mutationsOfType(m1);
}
5 late() { 
	g = p1.sampleIndividuals(200).genomes;
	g.outputVCF("./test.vcf");
	sim.simulationFinished();}