void hwe::run(funkyPars *pars){
if(doHWE==0)
return;
// pars->hweStruct = new funkyHWE;//old
funkyHWE *hweStruct = new funkyHWE;//new
double *freq = new double[pars->numSites];
double *F = new double[pars->numSites];
double *like0 = new double[pars->numSites];
double *likeF = new double[pars->numSites];
double **loglike3;
loglike3=angsd::get3likes(pars);
for(int s=0;s<pars->numSites;s++){
if(pars->keepSites[s]==0)
continue;
//start parameter
double x[2];
x[0]=0.05;
x[1]=0.05;
estHWE(x,loglike3[s],pars->nInd);
freq[s]=x[0];
F[s]=x[1];
likeF[s] = HWE_like(x,loglike3[s],pars->nInd);
x[1]=0.0;
x[0]=pars->results->asso->freq[s];
like0[s] = HWE_like(x,loglike3[s],pars->nInd);
// fprintf(stderr,"%f\t%f\n",x[0],x[1]);
//fprintf(stderr,"%f\t%f\t%f\n",loglike3[s][0],loglike3[s][1],loglike3[s][2]);
}
//old
// pars->hweStruct->freq=freq;
// pars->hweStruct->F=F;
hweStruct->freq=freq;
hweStruct->F=F;
hweStruct->like0=like0;
hweStruct->likeF=likeF;
pars->extras[index] = hweStruct;
for(int s=0;s<pars->numSites;s++)
delete[] loglike3[s];
delete[] loglike3;
}
void abcHWE::run(funkyPars *pars){
if(doHWE==0)
return;
funkyHWE *hweStruct = new funkyHWE;
double *freq = new double[pars->numSites];
double *freqHWE = new double[pars->numSites];
double *F = new double[pars->numSites];
double *like0 = new double[pars->numSites];
double *likeF = new double[pars->numSites];
double **loglike3;
loglike3=angsd::get3likesRescale(pars);
for(int s=0;s<pars->numSites;s++){
if(pars->keepSites[s]==0)
continue;
//est under HWE
freqHWE[s] = angsd::estFreq(loglike3[s],pars->nInd);
//start parameter
double x[2];
x[1]=0.0; //F
x[0]=freqHWE[s]; // freq
//log like for HWE freq
like0[s] = HWE_like(x,loglike3[s],pars->nInd);
//start parameter for EM_F
x[0]=freqHWE[s];
x[1]=0.05;
estHWE(x,loglike3[s],pars->nInd);
freq[s]=x[0];
F[s]=x[1];
likeF[s] = HWE_like(x,loglike3[s],pars->nInd);
// fprintf(stderr,"%f\t%f\n",x[0],x[1]);
//fprintf(stderr,"%f\t%f\t%f\n",loglike3[s][0],loglike3[s][1],loglike3[s][2]);
float lrt= 2*like0[s]-2*likeF[s];
if(lrt<0)
lrt=0;
if(lrt<LRT_thres)
pars->keepSites[s] =0;
}
hweStruct->freq=freq;
hweStruct->freqHWE=freqHWE;
hweStruct->F=F;
hweStruct->like0=like0;
hweStruct->likeF=likeF;
pars->extras[index] = hweStruct;
for(int s=0;s<pars->numSites;s++)
delete[] loglike3[s];
delete[] loglike3;
}
