void calc_stat(int begI,int endI,perChr &pc,kstring_t &str,int nChr){
double tW = slice(begI,endI,pc.tW);
double tP = slice(begI,endI,pc.tP);
double tF = slice(begI,endI,pc.tF);
double tH = slice(begI,endI,pc.tH);
double tL = slice(begI,endI,pc.tL);
ksprintf(&str,"%f\t%f\t%f\t%f\t%f\t",tW,tP,tF,tH,tL);
double tajima=tajd(nChr,tW,tP);
double fuf = fulif(nChr,tW,tF,tP);
double fud = fulid(nChr,tW,tF);
double fayh_val = fayh(nChr,tW,tH,tP);
double zeng_val = zenge(nChr,tW,tL);
// fprintf(stderr,"%f\n",tajima);
ksprintf(&str,"%f\t%f\t%f\t%f\t%f",tajima,fuf,fud,fayh_val,zeng_val);
}
void statsms::readms (string filename){
ifstream inp (filename.c_str());
if (!inp.is_open()){
cerr << "Error reading file "<< filename <<endl;
exit(1);
}
string line;
int linenum = 0;
int chrindex = 0;
int snpindex = 0;
int nsnp = 0;
double totalw = 0;
ofstream snpfs (snpfile.c_str());
int totalsnps = 0;
vector<int> nsegsites (nsamples,0);
int totalnind = 0 ;
vector<int> nind (nsamples,0);
for (int i = 0 ; i < nsamples; i++) {
nind[i] = samples[i];
totalnind += nind[i];
}
char ** snpmat = new char*[totalnind];
double **freq = new double*[nsamples];
double **td = new double *[nsamples];
double **thetaw = new double *[nsamples];
for (int i = 0 ; i < nsamples; i++) {
td[i] = new double[reps];
thetaw[i] = new double[reps];
}
double abba = 0 ;
double baba = 0 ;
double abba2 = 0 ;
double baba2 = 0 ;
double fstnum = 0;
double fstdenom = 0;
double l2yn = 0 ;
double l2en = 0;
double l2denom = 0;
vector<int> pop1nd10 (nind[0]+1,0);
vector<int> pop1nd01 (nind[0]+1,0);
vector<int> pop2nd10 (nind[1]+1,0);
vector<int> pop2nd01 (nind[1]+1,0);
vector<int> pop1nd00 (nind[0]+1,0);
vector<int> pop2nd00 (nind[1]+1,0);
vector<int> pop1nd11 (nind[0]+1,0);
vector<int> pop2nd11 (nind[1]+1,0);
vector<int> pop1n1 (nind[0]+1,0);
vector<int> pop2n1 (nind[0]+1,0);
vector<int> pop1d1 (nind[0]+1,0);
vector<int> pop2d1 (nind[1]+1,0);
vector<int> pop1n0 (nind[0]+1,0);
vector<int> pop2n0 (nind[0]+1,0);
vector<int> pop1d0 (nind[0]+1,0);
vector<int> pop2d0 (nind[1]+1,0);
vector<double> chrabba = vector<double>(reps,0);
vector<double> chrbaba = vector<double>(reps,0);
vector<double> chrsnps = vector<double>(reps,0);
vector<double> chrfstnum = vector<double> (reps,0);
vector<double> chrfstdenom = vector<double> (reps,0);
vector<double> chrw = vector<double> (reps,0);
int totalnsnps = 0;
int rep = 0 ;
int index = 0;
string id;
while ( std::getline (inp, line)){
linenum ++;
io::println ("line = " + line, 2);
char c = line[0];
if (c=='#')
continue;
if (line.empty())
continue;
if ( line.find ("segsites:")==0) {
string l1 = line.substr(9,line.length()-9);
nsnp = atoi (l1.c_str());
for (int i = 0 ; i < totalnind ; i++) {
snpmat[i] = new char[nsnp];
}
for (int i = 0 ; i < nsamples; i++){
freq[i] = new double[nsnp];
}
io::println ("SNPs = " + tostring(nsnp),2);
}
if ( line.find ("positions:")==0) {
vector<double> genmap ;
vector<double> physmap;
vector<string> snpids;
vector<vector<int> > geno;
vector<vector<int> > haplo;
chrindex ++;
string l1 = line.substr(10,line.length()-10);
//cout << "l1 = " << l1 << endl;
//
io::println ("rep = " + tostring(rep),2);
//cout << " rep = " << rep << endl;
rep++;
istringstream ss (line.substr(10,line.length()-10));
int count = 0 ;
while (!ss.eof()){
double pos;
ss>>pos;
// cout << pos << endl;
double ppos = pos * length;
double gpos = ppos * rho;
if (count >= nsnp )
break;
count++;
genmap.push_back (gpos);
physmap.push_back (ppos);
id = "snp" + tostring(index);
snpids.push_back (id);
index++;
}
for (int i = 0 ; i < totalnind ; i ++){
string s1, s2;
std::getline (inp, s1);
for (int j = 0 ; j < nsnp ; j++) {
snpmat[i][j] = s1[j];
}
}
vector<int> nsegsites(nsamples,0);
vector<double> pi(nsamples, 0 );
vector<double> h(nsamples,0);
vector<double> th(nsamples,0);
for (int i = 0, t = 0 ; i < nsamples; i++){
for (int j = 0 ; j < nsnp; j++){
freq[i][j] = frequency('1', j, samples[i], snpmat+t)/((double)samples[i]);
nsegsites[i] += (freq[i][j] > 0 && freq[i][j] < 1.0);
}
t += samples[i];
}
chrsnps[rep-1] = nsnp;
totalnsnps += nsnp;
for (int j = 0 ; j < nsnp ; j++) {
if (nsamples >= 5 ) {
if (ascertain.compare ("african")==0) {
if (freq[2][j] == 0 && freq[3][j] == 0 && freq[4][j] ==0 && freq[1][j]==0)
continue;
}
}
if (freq[2][j]>=1){
abba += freq[1][j] * ( 1-freq[0][j]);
baba += freq[0][j] * ( 1-freq[1][j]);
chrabba[rep-1] += freq[1][j] * ( 1-freq[0][j]);
chrbaba [rep-1] += freq[0][j] * ( 1-freq[1][j]);
}
if (freq[2][j]>0){
int ind = round(freq[0][j]*samples[0]);
pop1n1[ind]++;
ind = round(freq[1][j]*samples[1]);
pop2n1[ind]++;
} else {
int ind = round(freq[0][j]*samples[0]);
pop1n0[ind]++;
ind = round(freq[1][j]*samples[1]);
pop2n0[ind]++;
}
if (nsamples >= 4 ) {
if (freq[3][j]>=1){
abba2 += freq[1][j] * ( 1-freq[0][j]);
baba2 += freq[0][j] * ( 1-freq[1][j]);
}
if (freq[3][j] > 0 ) {
int ind = round(freq[0][j]*samples[0]);
pop1d1[ind]++;
ind = round(freq[1][j]*samples[1]);
pop2d1[ind]++;
} else {
int ind = round(freq[0][j]*samples[0]);
pop1d0[ind]++;
ind = round(freq[1][j]*samples[1]);
pop2d0[ind]++;
}
// cout << "here1" << endl;
if (freq[2][j]>0 && freq[3][j]==0) {
int ind = round(freq[0][j]*samples[0]);
pop1nd10[ind]++;
// cout << "here2\t" << ind << "\t" << freq[0][j] << "\t" << samples[0]<< endl;
ind = round(freq[1][j]*samples[1]);
pop2nd10[ind]++;
}
if (freq[3][j]>0 && freq[2][j]==0) {
int ind = round(freq[0][j]*samples[0]);
pop1nd01[ind]++;
// cout << "here3\t" << ind << "\t" << freq[0][j] << "\t" << samples[0]<< endl;
ind = round(freq[1][j]*samples[1]);
pop2nd01[ind]++;
}
if (freq[2][j]==0 && freq[3][j]==0) {
int ind = round(freq[0][j]*samples[0]);
pop1nd00[ind]++;
ind = round(freq[1][j]*samples[1]);
pop2nd00[ind]++;
}
if (freq[2][j]>0 && freq[3][j]>0) {
int ind = round(freq[0][j]*samples[0]);
pop1nd11[ind]++;
ind = round(freq[1][j]*samples[1]);
pop2nd11[ind]++;
}
}
if (freq[0][j]<=0 &&& freq[1][j]>0 && freq[1][j]<1) {
l2en +=pow (freq[0][j] - freq[2][j],2);
l2yn +=pow (freq[1][j] - freq[2][j],2);
l2denom ++;
}
int n0 = samples[0];
int n1 = samples[1];
int a0 = freq[0][j] * n0;
int a1 = freq[1][j] * n1 ;
double w = 1;
double f0 = freq[0][j];
double f1 = freq[1][j];
if (ascertain.compare("hetinb")==0) {
a1 --; // Account for ascertainment
n1 -= 2;
f1 = ((double)a1)/n1;
w = 2*freq[1][j]*(1-freq[1][j]);
} else if (ascertain.compare("outgroup")==0) {
if (freq[2][j]>0)
w = 1 ;
else
w = 0;
} else if (ascertain.compare ("all")==0) {
w = 1;
} else if (ascertain.compare ("hetinout") == 0) {
w = freq[2][j]*(1-freq[2][j]);
} else if (ascertain.compare ("polyinb")==0) {
if (freq[1][j]>0 && freq[1][j] < 1 ) w = 1;
else w = 0;
} else if (ascertain.compare ("polyinanb")==0){
if (freq[1][j]>0 && freq[1][j] < 1 && freq[0][j] > 0 && freq[0][j] < 1) w = 1;
else w = 0;
} else if (ascertain.compare ("polyinaorb")==0) {
if ((freq[1][j]>0 && freq[1][j] < 1)||(freq[0][j] > 0 && freq[0][j] < 1)) w = 1;
else w = 0;
} else if (ascertain.compare ("polyina")==0) {
if (freq[0][j]>0 && freq[0][j] < 1 ) w = 1;
else w = 0;
} else if (ascertain.compare ("hetina")==0) {
a0 --; // Account for ascertainment
n0 -= 2;
f0 = ((double)a0)/n0;
w = 2*freq[0][j]*(1-freq[0][j]);
}
double h0 = 0 ;
double h1 = 0 ;
if (n0 > 1)
h0 = a0*(n0-a0)/(n0*(n0-1.));
if (n1 > 1)
h1 = a1*(n1-a1)/(n1*(n1-1.));
double fstn = pow((f0-f1),2) - h0/n0 - h1/n1;
double fstd = fstn + h0 + h1;
fstnum += fstn * w;
fstdenom += fstd * w;
chrfstnum[rep-1] += fstn * w;
chrfstdenom[rep-1] += fstd * w;
chrw[rep-1] += w;
totalw += w;
}
for (int i = 0 , t = 0 ; i < nsamples; i++) {
pi[i] = nucdiv (samples[i], nsnp, snpmat +t );
h[i] = hfay (samples[i], nsnp, snpmat +t );
th[i] = thetah (samples[i], nsnp, snpmat +t );
td [i][rep-1] = tajd(samples[i], nsegsites[i], pi[i]);
thetaw[i][rep-1] = nsegsites[i]/(2*a1f(samples[i]));
t += samples[i];
}
for (int i = 0 ; i < nsamples; i++)
delete[] freq[i];
for (int i = 0 ; i < totalnind; i++)
delete[] snpmat[i];
if (printsnplist) {
for (int j =0 ; j < nsnp; j++){
snpfs << snpids[j] << "\t" << chrindex << "\t" << genmap[j] << "\t" << physmap[j] << endl;
}
}
} // One set of MS sims
if (io::debug >= 2) {
cout << "Next MS sim " <<endl;
}
}
/*********************************************************
* *
* Main Function *
* ------------- *
* *
*********************************************************
| Takes arguments and launches the gof simulations. |
*-------------------------------------------------------*/
int main(int argc, char *argv[]) // Array of char=arguments line
{
//--- Declarations & Call Function ---//
int i=0, j=0, k=0, count=0, howmany=0, segsites=0, okim=0, oksim=0, numsim=0, totsim=0, nokl=0, nokl0=0;
int **statseg=NULL, **nbvariant=NULL, oks[3], okstot[3];
FILE *pf=NULL, *fopen(const char*, const char*); // Pointer on File for outputs (pf) and IM input file
double tajd();
char **list=NULL; // Haplotype list
void updatemainparams(struct params*);
int gensam(struct params*, char**, int**, int*);
int **imatrix(int, int);
//// From rand1.c ////
/* Celine changed 03/18/2010 */
void seedit(char*, FILE*, struct params *);/*/////*/
char **cmatrix(int, int);
//// From params.c ////
void changeparams(struct params*);
void changeparamslocus(struct params*, int);
struct params getpars(int, char*[], int*);
//--- Structure declaration---//
struct params param;
//--- Get arguments ---//
param=getpars(argc, argv, &howmany); // Get input by user for parameters
pf=stdout; // Output
/* Celine changed 03/18/2010 */
if( !param.commandlineseedflag ) seedit("s", pf, ¶m);// WRITE seeds in summary output file
/*/////*/
/* Uncommented for Celine's use */
/* for(i=0;i<argc;i++) // Information on simulation
fprintf(pf, "%s ", argv[i]);
*/////\
//---------- Initialisation & Memory allocation ------------------//
nbvariant=imatrix(param.cp.npop+1, maxsites); // array of nb of frequency spectrum
typeseg=(int*)malloc((unsigned)(maxsites*sizeof(int))); // type of sites
statseg=imatrix(param.cp.npop+3, howmany); // Records locus specific S1, S2, Ss, Sf,
changeparams(¶m); // Change estimates parameters from priors
updatemainparams(¶m); // Update parameters for the coalescent
oksim=totsim=okstot[0]=okstot[1]=okstot[1]=okstot[2]=0; // simulation check, total #of sim, check on statistics for all simulations
for(numsim=0; numsim<param.cp.nsim;numsim++) // Loop along number of simulations for this set of parameters
{
//--- Initialization and reset of quality checks ---//
count=nokl=nokl0=okim=oks[0]=oks[1]=oks[1]=oks[2]=0; // number of loci, # loci with ok genealogies, no set sites, #statistics ok
for(i=0;i<11;i++) // Sim specific Stats
param.cp.sSiFst[i]=0;
//--- Loop along the loci in the simulation ---//
while((howmany-count++))
{
if(okim==0) // Case All loci ok in the sample
{
for(i=0;i<11;i++)
{
param.cp.lSiFst[i]=0.0;
if(i<9)
param.lp[count-1].tpH[i]=0;
}
changeparamslocus(¶m, count-1); // Get locus specific parameters
list=cmatrix(param.cp.nsam, maxsites+1); // Allocate list of haplotypes
segsites=gensam(¶m, list, nbvariant, param.lp[count-1].S);// Generate a new gene ARG
statseg[0][count-1]=segsites; // Total number of seg sites in sample
for(i=1;i<3+param.cp.npop;i++)
statseg[i][count-1]=0;
if((segsites>0)) // Case segsite>0: get stats
{
/* fprintf(pf, "segsites:%d\npositions:\n",segsites); */
/* for(i=0;i<param.cp.nsam;i++) fprintf(pf, "%s\n", list[i]); */
/* fprintf(pf, "\n"); */
if(segsites<=param.cp.nsites) // Case segsite < lenght of locus
{
for(k=0;k<param.cp.nsam;k++)
{
for(i=k+1;i<param.cp.nsam;i++)
{
if((k<param.lp[count-1].ni[1])&&(i<param.lp[count-1].ni[1])) // pop1
{
param.lp[count-1].tpH[0]++; // # chromosomes
for(j=0;j<segsites;j++)
{
if(list[k][j]!=list[i][j])
param.lp[count-1].tpH[1]++; // # seg sites
}
}
else if((k>=param.lp[count-1].ni[1])&&(i>=param.lp[count-1].ni[1])) // pop2
{
param.lp[count-1].tpH[2]++; // # chromosomes
for(j=0;j<segsites;j++)
{
if(list[k][j]!=list[i][j])
param.lp[count-1].tpH[3]++; // # seg sites
}
}
else // total sample
{
param.lp[count-1].tpH[4]++;; // Totsal sample size
for(j=0;j<segsites;j++)
{
if(list[k][j]!=list[i][j])
param.lp[count-1].tpH[5]++; // total S
}
}
}// Loop on chromosome
}// Loop along all sampled sequence for the locus
for(i=0;i<segsites;i++) // Calulate S statistics for the locus
{
if(typeseg[i]<0) statseg[3][count-1]++; // shared
else if(typeseg[i]<param.cp.npop+1) statseg[typeseg[i]][count-1]++; // population specific
else statseg[4][count-1]++; // fixed
}
for(i=1;i<5;i++) //--- Record S1 S2 Ss Sf forthe locus ---//
param.cp.lSiFst[i-1]+=statseg[i][count-1];
for(i=0;i<param.cp.nsam;i++) // Free memory for this locus
free(list[i]);
free(list);
}// End case segsite<lenght of locus
else // Case segsites>lenght of locus
{
okim=1; // Sample have a wrong locus
oksim=1; // stop this simulation
break;
}
}// End locus polymorphic
else // Locus without seg sites
{
okim=1; // Sample have a wrong locus (S=0)
oksim=2; // 0 for all stats
}
}// End Sample good until now
if(okim==0) // All loci good until now
{
nokl++; // +1 good locus
nokl0++; // +1 polymorphic locus
for(i=0;i<7;i++)
{
if(i<4)
param.cp.sSiFst[i]+=param.cp.lSiFst[i]; // sum of Sk
param.lp[count-1].H[i]=param.lp[count-1].tpH[i]; // locus specific stats
}
param.cp.lSiFst[5]=param.lp[count-1].H[1]/=param.lp[count-1].H[0]; // Hw1
param.cp.lSiFst[6]=param.lp[count-1].H[3]/=param.lp[count-1].H[2]; // Hw2
param.lp[count-1].H[5]/=param.lp[count-1].H[4]; // Hb
param.cp.lSiFst[4]=param.lp[count-1].H[6]=1-((param.lp[count-1].H[1]+param.lp[count-1].H[3])/2)/ param.lp[count-1].H[5];// locis specific Fst
if((param.lp[count-1].S[0]>0)&&(param.lp[count-1].ni[1]>2)) // Locus popymorphic in pop1
{
param.cp.lSiFst[7]=tajd(param.lp[count-1].ni[1], param.lp[count-1].S[0], param.lp[count-1].H[1]);
param.cp.sSiFst[7]+=param.cp.lSiFst[7];
oks[0]++; // +1 good stat for pop1
}
if((param.lp[count-1].S[1]>0)&&(param.lp[count-1].ni[2]>2)) // Locus popymorphic in pop2
{
param.cp.lSiFst[8]=tajd(param.lp[count-1].ni[2], param.lp[count-1].S[1], param.lp[count-1].H[3]);
param.cp.sSiFst[8]+=param.cp.lSiFst[8];
oks[1]++; // +1 good stat for pop2
}
if(statseg[1][count-1]>0) // Locus popymorphic private in pop1
param.lp[count-1].H[7]=param.cp.lSiFst[9]+=(double) param.lp[count-1].S[2]/(statseg[1][count-1]*param.lp[count-1].ni[1]*2); // p(1)
if(statseg[2][count-1]>0) // Locus popymorphic private in pop2
param.lp[count-1].H[7]=param.cp.lSiFst[9]+=(double) param.lp[count-1].S[3]/(statseg[2][count-1]*param.lp[count-1].ni[2]*2); // p(1)
param.cp.sSiFst[9]+=param.cp.lSiFst[9]; // sum p1
if(statseg[3][count-1]>0) // Locus popymorphic private in pop2
{
param.lp[count-1].H[8]=param.cp.lSiFst[10]=(double) param.lp[count-1].S[4]/(statseg[3][count-1]*(param.lp[count-1].ni[2]+param.lp[count-1].ni[1])); // p(2)
param.cp.sSiFst[10]+=param.cp.lSiFst[10]; // sum p2
oks[2]++;
}
param.cp.sSiFst[4]+=param.lp[count-1].H[6]; // sum Fst
param.cp.sSiFst[5]+=param.lp[count-1].H[1]; // sum Hw1
param.cp.sSiFst[6]+=param.lp[count-1].H[3]; // sum Hw2
}
else if(oksim==2) // Case no seg site for that locus
{
oksim=0; // reset checks
okim=0;
nokl++; // 1+ locus to count in mean (all 0 values)
for(i=0;i<9;i++)
param.lp[count-1].H[i]=param.lp[count-1].tpH[i]; // locus specific stats
}
}// End loop on loci
if(nokl==howmany) // All sample good
{
totsim++; // 1+ good simulation
for(i=0;i<4;i++)
param.cp.SiFst[i]+=param.cp.sSiFst[i]; // sum of S stats along simulations
for(i=4;i<11;i++)
{
if(((i<7)||(i>=9))&&(nokl0>0))
param.cp.SiFst[i]+=(double)param.cp.sSiFst[i]/nokl0; // mean of other stats along simulations
if((i>=7)&&(i<9)&&(oks[i-7]>0))
{
param.cp.SiFst[i]+=(double)param.cp.sSiFst[i]/oks[i-7];
okstot[i-7]++;
}
}
}
}// End loop on simulations
if(oksim==0) // All simulations worked
{
/* Uncommented for Celine's use */
/* for(i=0;i<11;i++) */////
for(i=0;i<9;i++)
{
if((i<7)||(i>=9))
fprintf(pf, "%lg\t", (double) param.cp.SiFst[i]/(totsim)); // write mean of sum of S stats, Fst and Hws over simulations
if((i>=7)&&(i<9))
{
if(oks[i-7]>0)
fprintf(pf, "%lg\t", (double) param.cp.SiFst[i]/(okstot[i-7])); // write mean Tds if S>0 in pops
else fprintf(pf, "NA\t" );
}
}
fprintf(pf, "\n");
}
else // Case one locus with too much seg sites
{
for(i=0;i<9;i++)
fprintf(pf, "NA\t" );
fprintf(pf, "\n");
}
/* Celine changed 03/18/2010 */
seedit("end", pf, ¶m); // in randx.c, flag[0]!="s" so create/rewrite seed in seedmimar
/*/////*/
fclose(pf);
free(typeseg);
for(i=0;i<param.cp.npop+3;i++)
{
if(i<param.cp.npop+1)
free(nbvariant[i]);
free(statseg[i]);
}
free(nbvariant);
free(statseg);
///////// FREE PARAM ///////
for(i=0;i<param.cp.npop;i++)
free(param.cp.mig_mat[i]);
free(param.cp.mig_mat);
free(param.cp.config);
/* Celine changed 11/27/2009 */
for(i=9;i>=0;i--)
if(param.cp.listevent[i]!=NULL && param.cp.listevent[i]->nextde!=NULL)
free(param.cp.listevent[i]->nextde);
if(param.cp.listevent!=NULL)
free(param.cp.listevent);
/*/////*/
free(param.cp.deventlist);
free(param.cp.size);
free(param.cp.alphag);
for(i=0;i<3;i++)
free(param.cp.uniform[i]);
free(param.cp.uniform);
free(param.cp.oldest);
free(param.cp.newest);
free(param.cp.newparam);
/* Celine changed 11/27/2009 */
for(i=0;i<howmany;i++)
free(param.lp[i].name);
/*/////*/
free(param.lp);
/* Celine changed 03/18/2010 */
free( param.tableseeds); /*/////*/
exit(0);
}// End main function
