void majorminor::run(funkyPars *pars){
if(doMajorMinor==0 || doMajorMinor ==3 )
return;
if(doMajorMinor==1 && pars->likes==NULL){
fprintf(stderr,"[%s.%s():%d] Problem here:\n",__FILE__,__FUNCTION__,__LINE__);
exit(0);
}
//allocate and initialize
pars->major = new char [pars->numSites];
pars->minor = new char [pars->numSites];
memset(pars->major,4,pars->numSites);
memset(pars->minor,4,pars->numSites);
if(doMajorMinor!=2)
majorMinorGL(pars);
else if(doMajorMinor==2)
majorMinorCounts(pars->counts,pars->nInd,pars->numSites,pars->major,pars->minor,pars->keepSites);
else
fprintf(stderr,"[%s.%s()%d] Should never happen\n",__FILE__,__FUNCTION__,__LINE__);
//if user has requested reference/ancestral as major then swap if needed
if(doMajorMinor==4||doMajorMinor==5)
modMajorMinor(pars,doMajorMinor);
}
void abcMajorMinor::run(funkyPars *pars){
if(doMajorMinor==0 || doMajorMinor ==3 )
return;
if(doMajorMinor==1 && pars->likes==NULL){
fprintf(stderr,"[%s.%s():%d] Problem here:\n",__FILE__,__FUNCTION__,__LINE__);
exit(0);
}
//allocate and initialize
pars->major = new char [pars->numSites];
pars->minor = new char [pars->numSites];
memset(pars->major,4,pars->numSites);
memset(pars->minor,4,pars->numSites);
if(doMajorMinor!=2)
majorMinorGL(pars,doMajorMinor);
else if(doMajorMinor==2)
majorMinorCounts(pars->counts,pars->nInd,pars->numSites,pars->major,pars->minor,pars->keepSites,doMajorMinor,pars->ref,pars->anc);
else
fprintf(stderr,"[%s.%s()%d] Should never happen\n",__FILE__,__FUNCTION__,__LINE__);
if(doSaf!=0&&pest!=NULL){
//fix case of triallelic site in pest output when doing pest
for(int s=0;s<pars->numSites;s++){
if(pars->keepSites[s]==0)
continue;
int a=refToInt[pars->anc[s]];
int b=refToInt[pars->major[s]];
int c=refToInt[pars->major[s]];
if(a!=b&&a!=c)
pars->keepSites[s]=0;
}
}
//if user has requested reference/ancestral then it is done in majorMinorGL and majorMinorCounts 0.585
/*
if(doMajorMinor==4||doMajorMinor==5)
modMajorMinor(pars,doMajorMinor);
*/
}
void abcMajorMinor::run(funkyPars *pars){
if(doMajorMinor==0 || doMajorMinor ==3 )
return;
if(doMajorMinor==1 && pars->likes==NULL){
fprintf(stderr,"[%s.%s():%d] Problem here:\n",__FILE__,__FUNCTION__,__LINE__);
exit(0);
}
//allocate and initialize
pars->major = new char [pars->numSites];
pars->minor = new char [pars->numSites];
memset(pars->major,4,pars->numSites);
memset(pars->minor,4,pars->numSites);
if(doMajorMinor!=2)
majorMinorGL(pars,doMajorMinor);
else if(doMajorMinor==2)
majorMinorCounts(pars->counts,pars->nInd,pars->numSites,pars->major,pars->minor,pars->keepSites,doMajorMinor,pars->ref,pars->anc);
else
fprintf(stderr,"[%s.%s()%d] Should never happen\n",__FILE__,__FUNCTION__,__LINE__);
if(doSaf!=0&&pest!=NULL&&skipTriallelic==1){
//fix case of triallelic site in pest output when doing pest
for(int s=0;s<pars->numSites;s++){
if(pars->keepSites[s]==0)
continue;
int a=refToInt[pars->anc[s]];
int b=refToInt[pars->major[s]];
int c=refToInt[pars->minor[s]];
if(a!=b&&a!=c)
pars->keepSites[s]=0;
}
}
//if user has requested reference/ancestral then it is done in majorMinorGL and majorMinorCounts 0.585
/*
if(doMajorMinor==4||doMajorMinor==5)
modMajorMinor(pars,doMajorMinor);
*/
if(doGlf==2||doVcf>0){
lh3struct *lh3 = new lh3struct;
pars->extras[index] = lh3;
lh3->hasAlloced = new char[pars->numSites];
memset(lh3->hasAlloced,0,pars->numSites);
lh3->lh3 = new double *[pars->numSites];
for(int s=0;s<pars->numSites;s++) {
if(pars->keepSites[s]==0)
continue;
int major = pars->major[s];
int minor = pars->minor[s];
assert(major!=4&&minor!=4);
lh3->hasAlloced[s]=1;
lh3->lh3[s] = new double[3*pars->nInd];
for(int i=0;i<pars->nInd;i++) {
double val[3];
val[0] = pars->likes[s][i*10+angsd::majorminor[major][major]];
val[1] = pars->likes[s][i*10+angsd::majorminor[major][minor]];
val[2] = pars->likes[s][i*10+angsd::majorminor[minor][minor]];
if(isnan(val,3)){
pars->keepSites[s]=0;
break;
}
angsd::logrescale(val,3);
lh3->lh3[s][i*3+0]=val[0];
lh3->lh3[s][i*3+1]=val[1];
lh3->lh3[s][i*3+2]=val[2];
}
}
}
}
