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main_psmc.h
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main_psmc.h
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#pragma once
#include "psmcreader.h"
#include "fastas.h"
//from psmc
typedef struct{
int n; // $n$ in psmc.tex. number of intervals equals to $n+1$
int n_free; // number of free lambdas
int *par_map; // parameter groups
char *pattern;
double *times;//<-splittimes
double *params;//<- effective population sizes
double TR[2];
double MT;
}psmc_par;
typedef struct{
std::vector<double> eN1;
std::vector<double> eN2;
double rho[2];
double theta;
}msarg;
typedef struct {
int nChr;
char *chooseChr;
int start;
int stop;
size_t nSites;
int maxIter;
double tole;
perpsmc * perc;
char *fname;
int onlyOnce;
long seed;//<-seed=-1 old version;seed=0 means time; othervise it will be used as seed
int blocksize; //in bp
psmc_par *par;
perFasta *pf;
int RD;
int nThreads;
int nIter;
int doLinear;
double init;
char *msstr;
msarg msstr_arg;
char *psmc_infile;
double init_theta;
double init_rho;
double init_max_t;
int dospline;
}args;
args * getArgs(int argc,char **argv,int dontprint);
void destroy_args(args *p);
int main_psmc(int argc,char **argv);