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multipop.cpp
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multipop.cpp
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#include <iostream>
#include <algorithm>
#include <fstream>
#include <string>
#include <cmath>
#include <math.h>
#include <cctype>
#include <unistd.h>
#include "Util.h"
#include "PostCalMultiPop.h"
#include "CaviarModelMultiPop.h"
using namespace std;
bool checkInputFiles(vector <string> zFiles, vector <string> ldFiles, string outputFileName) {
int size = 0;
if (zFiles.size() == 0 || ldFiles.size() ==0) {
cout << "You did not specify any LD file of Z file" << endl;
return (false);
} if (zFiles.size() != ldFiles.size()) {
cout << "The number of LD files and Z files do not match" << endl;
return (false);
}
//TODO: CHECK THE PARAMETER ARE CORRECT
return(true);
}
int main( int argc, char *argv[] ){
int oc = 0;
int snpCount = 0;
double NCP = 5.7;
double rho = 0.95;
int totalCausalSNP = 2;
bool histFlag;
vector <string> ldFiles;
vector <string> zFiles;
string outputFileName = "";
while ((oc = getopt(argc, argv, "vhl:o:z:r:c:f:")) != -1) {
switch (oc) {
case 'v':
cout << "version 2.0:" << endl;
case 'h':
cout << "Options: " << endl;
cout << "-h, --help show this help message and exit " << endl;
cout << "-o OUTFILE, --out=OUTFILE specify the output file" << endl;
cout << "-l LDFILE, --ld_file=LDFILE the ld input file" << endl;
cout << "-z ZFILE, --z_file=ZFILE the z-score and rsID files" << endl;
cout << "-r RHO, --rho-prob=RHO set $pho$ probability " << endl;
cout << "-c causal set the maximum number of causal SNPs" << endl;
cout << "-f 1 to out the probaility of different number of causal SNP" << endl;
cout << "Example 2 populcations command:" << endl;
cout << "./mupCAVIAR -l <LDFILE1> -l <LDFILE2> -z <ZFILE1> -z <ZFILE2> -r 0.95 -f <NUMCAUSAL> -o <OUTPUTFILE>" << endl;
cout << "Example 3 populcations command:" << endl;
cout << "./mupCAVIAR -l <LDFILE1> -l <LDFILE2> -l <LDFILE3> ";
cout << " -z <ZFILE1> -z <ZFILE2> -z <ZFILE3> -r 0.95 -f <NUMCAUSAL> -o <OUTPUTFILE>" << endl;
return(0);
case 'l':
ldFiles.push_back(string(optarg));
break;
case 'o':
outputFileName = string(optarg);
break;
case 'z':
zFiles.push_back(string(optarg));
break;
case 'r':
rho = atof(optarg);
break;
case 'c':
totalCausalSNP = atoi(optarg);
break;
case 'f':
histFlag = true;
break;
case ':':
case '?':
default:
cout << "Strange" << endl;
break;
}
}
//program is running
cout << "@-------------------------------------------------------------@" << endl;
cout << "| MultiplePopAVIAR! | v2.0 | 25/Aug/2017 | " << endl;
cout << "|-------------------------------------------------------------|" << endl;
cout << "| (C) 2017 Farhad Hormozdiari, GNU General Public License, v2 |" << endl;
cout << "|-------------------------------------------------------------|" << endl;
cout << "| For documentation, citation & bug-report instructions: |" << endl;
cout << "| http://genetics.cs.ucla.edu/caviar/ |" << endl;
cout << "@-------------------------------------------------------------@" << endl;
//Check the input is right?
if( !checkInputFiles(zFiles, ldFiles, outputFileName) )
return(0);
CaviarModelMultiPop gwasModel(ldFiles, zFiles, outputFileName, totalCausalSNP, NCP, rho, histFlag);
gwasModel.run();
gwasModel.finishUp();
return 0;
}