Scenario 2 : random mating for 10 generations within 2 populations, then cross these 2 populations and random mating for 10 generations
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%%file main.cpp
#include <iostream>
#include <fstream>
#include "cohort.h"
#include "tools.h"
#include "simPop.h"
#include "global.h"
#include "parmMap.h"
int main(int argc, const char * argv[])
{
///user-defined parameters and map positions
unsigned popSize = 10;
unsigned nGen = 10;
string genomeFile="/Users/erxingfangshui/Dropbox/GenSim/GenSim1.3_xcode/genomeInfo.txt";
string mapFile="/Users/erxingfangshui/Dropbox/GenSim/GenSim1.3_xcode/mapPos.txt";
string haplotype="/Users/erxingfangshui/Dropbox/GenSim/GenSim1.3_xcode/haplotype.txt";
SimPop osim1(genomeFile,mapFile);
SimPop osim2(genomeFile,mapFile);
SimPop osim3(genomeFile,mapFile);
osim1.popFounders(popSize,haplotype);
osim2.popFounders(popSize,haplotype);
osim3.cross(osim1,osim2,popSize);
osim3.popSample(popSize/2,nGen);
MatrixXf out;
out=osim3.getGenotypes();
ofstream outFile("/Users/erxingfangshui/genotype.example");
outFile << out;
return 0;
}
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%%file main.cpp
#include <iostream>
#include <fstream>
#include "cohort.h"
#include "tools.h"
#include "simPop.h"
#include "global.h"
#include "parmMap.h"
int main(int argc, const char * argv[])
{
///constant nLoci, chrLength and random map positions
unsigned nLoci = 100;
unsigned nChrm = 1;
double chrLength = 0.01;
unsigned popSize = 100;
unsigned nGen = 10;
double mutRate = 1e-5;
SimPop osim1(nChrm,nLoci,chrLength,mutRate);
SimPop osim2(nChrm,nLoci,chrLength,mutRate);
SimPop osim3(nChrm,nLoci,chrLength,mutRate);
osim1.popFounders(popSize);
osim2.popFounders(popSize);
osim3.cross(osim1,osim2,popSize);
osim3.popSample(popSize/2,nGen);
MatrixXf out;
out=osim3.getGenotypes();
ofstream outFile("/Users/erxingfangshui/genotype.example");
outFile << out;
return 0;
}
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%%file makeGenSim
#############################################################################
# Makefile for building: OSim
INCPATH = -I/Users/erxingfangshui/Dropbox/CODE/eigen3 -I/Users/erxingfangshui/Dropbox/CODE/boost
GenSim: main.o libGenSim.a
g++ -o GenSim main.o libGenSim.a
main.o: main.cpp
g++ $(INCPATH) -c -o main.o main.cpp
clean:
\rm main.o GenSim
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%%bash
mv makeGenSim ../
mv main.cpp ../
cd ..
make -f makeGenSim
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%%bash
cd ..
./GenSim