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abcSaf.cpp
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#include <cstdio>
#include <cmath>
#include <assert.h>
#include <zlib.h>
#include <cfloat>
#include <htslib/kstring.h>
#include "abcFreq.h"
#include "shared.h"
#include "analysisFunction.h"
#include <pthread.h>
#include "abc.h"
#include "abcSaf.h"
#define MINLIKE -1000.0 //this is for setting genotypelikelhoods to missing (EXPLAINED BELOW)
void writeAllThetas(BGZF *dat,FILE *idx,char *tmpChr,int64_t &offs,std::vector<int> &p,std::vector<float> *res,int nChr){
assert(dat!=NULL);
assert(idx!=NULL);
assert(p.size()==res[0].size());
for(int i=1;i<5;i++)
assert(p.size()==res[i].size());//DRAGON, might be discarded during compilation
if(p.size()!=0&&tmpChr!=NULL){
//write clen and chromoname for both index and bgzf
size_t clen = strlen(tmpChr);
fwrite(&clen,sizeof(size_t),1,idx);
fwrite(tmpChr,1,clen,idx);
assert(sizeof(size_t)==bgzf_write(dat,&clen,sizeof(size_t)));
assert(clen==bgzf_write(dat,tmpChr,clen));
//write number of sites for both index and bgzf
size_t tt = p.size();
fwrite(&tt,sizeof(size_t),1,idx);
assert(sizeof(size_t)==bgzf_write(dat,&tt,sizeof(size_t)));
//write nChr for both index and bgzf
fwrite(&nChr,sizeof(int),1,idx);
assert(sizeof(int)==bgzf_write(dat,&nChr,sizeof(int)));
//write bgzf offset into idx
fwrite(&offs,sizeof(int64_t),1,idx);
for(int i=0;i<p.size();i++)
aio::bgzf_write(dat,&p[i],sizeof(int));
for(int i=0;i<5;i++)
for(int j=0;j<p.size();j++)
aio::bgzf_write(dat,&res[i][j],sizeof(float));
}
//reset
offs = bgzf_tell(dat);
p.clear();
for(int i=0;i<5;i++)
res[i].clear();
}
namespace filipe{
void algoJoint(double **liks,char *anc,int nsites,int numInds,int underFlowProtect, int fold,int *keepSites,realRes *r,int noTrans,int doSaf,char *major,char *minor,double *freq,double *indF,int newDim);
}
void abcSaf::printArg(FILE *argFile){
fprintf(argFile,"--------------\n%s:\n",__FILE__);
fprintf(argFile,"\t-doSaf\t\t%d\n",doSaf);
fprintf(argFile,"\t1: perform multisample GL estimation\n\t2: use an inbreeding version\n\t3: calculate genotype probabilities (use -doPost 3 instead)\n\t4: Assume genotype posteriors as input (still beta) \n");
fprintf(argFile,"\t-doThetas\t\t%d (calculate thetas)\n",noTrans);
fprintf(argFile,"\t-underFlowProtect\t%d\n",underFlowProtect);
fprintf(argFile,"\t-fold\t\t\t%d (deprecated)\n",fold);
fprintf(argFile,"\t-anc\t\t\t%s (ancestral fasta)\n",anc);
fprintf(argFile,"\t-noTrans\t\t%d (remove transitions)\n",noTrans);
fprintf(argFile,"\t-pest\t\t\t%s (prior SFS)\n",pest);
fprintf(argFile,"\t-isHap\t\t\t%d (is haploid beta!)\n",isHap);
fprintf(argFile,"\t-doPost\t\t\t%d (doPost 3,used for accesing saf based variables)\n",doPost);
fprintf(argFile,"NB:\n\t If -pest is supplied in addition to -doSaf then the output will then be posterior probability of the sample allelefrequency for each site\n");
}
void abcSaf::getOptions(argStruct *arguments){
doSaf=angsd::getArg("-doSaf",doSaf,arguments);
// if(doSaf==0)
// return;
doPost=angsd::getArg("-doPost",doPost,arguments);
isHap=angsd::getArg("-isHap",isHap,arguments);
pest = angsd::getArg("-pest",pest,arguments);
fold=angsd::getArg("-fold",fold,arguments);
if(doSaf==3){ //DRAGON
fprintf(stderr,"\t-> Please use -doPost 3 instead for -doSaf 3\n");
exit(0);
}
if(doSaf>0||doPost==3){
if(pest!=NULL){
if(fold==0)
prior=angsd::readDouble(pest,arguments->nInd*2+1);
else
prior=angsd::readDouble(pest,arguments->nInd+1);
int nd=arguments->nInd*2+1;
if(fold)
nd=arguments->nInd+1;
double tts=0;
for(int i=0;i<nd;i++)
tts += prior[i];
for(int i=0;i<nd;i++)
prior[i] = log(prior[i]/tts);
}
lbicoTab = new double[2*arguments->nInd+1];
tsktsktsk = 2*arguments->nInd+1;
myComb2Tab = new double*[2*arguments->nInd+1];
for(int i=0;i<2*arguments->nInd+1;i++){
lbicoTab[i] = angsd::lbico(2*arguments->nInd,i);
myComb2Tab[i] = new double[3];
for(int j=0;j<3;j++)
if(j<=i)
myComb2Tab[i][j] = angsd::myComb2(arguments->nInd,i,j);
}
if(isHap){
for(int i=0;i<arguments->nInd+1;i++)
lbicoTab[i] = angsd::lbico(arguments->nInd,i);
}
mynchr = 2*arguments->nInd;
if(fold)
mynchr = arguments->nInd;
}
noTrans = angsd::getArg("-noTrans",noTrans,arguments);
int GL = 0;
GL = angsd::getArg("-GL",GL,arguments);
doThetas= angsd::getArg("-doThetas",doThetas,arguments);
if(doSaf==0&&doThetas==0&doPost!=3)
return;
if(doThetas!=0&& doSaf==0){
fprintf(stderr,"\t Must estimate joint llh (-doSaf) when estimating thetas\n");
exit(0);
}
if(pest==NULL&& doThetas){
fprintf(stderr,"\t Must supply a sfs used as prior for estimating thetas\n");
exit(0);
}
underFlowProtect=angsd::getArg("-underFlowProtect",underFlowProtect,arguments);
int isSim =0;
isSim=angsd::getArg("-isSim",isSim,arguments);
if(doSaf==0)
return;
if(arguments->regions.size()>1)
fprintf(stderr,"\t-> !! You are doing -dosaf incombination with -rf, please make sure that your -rf file is sorted !!\n");
anc = angsd::getArg("-anc",anc,arguments);
if(doSaf && (anc==NULL&&isSim==0) ){
if(doSaf!=3 && doSaf!=5 ){
fprintf(stderr,"\t-> Must supply -anc for polarizing the spectrum\n");
exit(0);
}
}
if(doSaf==5){
int doMajorMinor =0;
doMajorMinor = angsd::getArg("-doMajorMinor",doMajorMinor,arguments);
if(doMajorMinor==0){
fprintf(stderr,"\t-> for -doSaf 5 you must infer major and minor\n");
exit(0);
}
}
int ai = arguments->inputtype;
if(GL==0 &&(ai!=INPUT_GLF && ai !=INPUT_GLF3 && ai !=INPUT_VCF_GL &&ai !=INPUT_BEAGLE&&ai!=INPUT_GLF10_TEXT)){
fprintf(stderr,"\t-> Must supply genotype likelihoods (-GL [INT])\n");
printArg(arguments->argumentFile);
exit(0);
}
if(doSaf==2){
fprintf(stderr,"\t-> (Using Filipe G Vieira modification of: %s)\n",__FILE__);
int doMajorMinor =0;
doMajorMinor = angsd::getArg("-doMajorMinor",doMajorMinor,arguments);
int doMaf =0;
doMaf = angsd::getArg("-doMaf",doMaf,arguments);
if(doMajorMinor==0||doMaf==0){
fprintf(stderr,"\t-> Must have major/minor and MAF for using the inbreeding version of realSFS\n");
exit(0);
}
char *indF_name = NULL;
indF_name = angsd::getArg("-indF",indF_name,arguments);
if(indF_name==NULL){
filipeIndF = new double[arguments->nInd];
for(int i=0;i<arguments->nInd;i++)
filipeIndF[i] =0;
fprintf(stderr,"\t-> No -indF file provided will assume an inbreeding zero for all samples.\n");
fprintf(stderr,"\t-> If no inbreeding is expected consider using -doSaf 1\n");
}else
filipeIndF = angsd::readDouble(indF_name,arguments->nInd);
}
if(doSaf==3){
fprintf(stderr,"\t-> Will call genotypes using sample allele frequencies\n");
int doMajorMinor =0;
doMajorMinor = angsd::getArg("-doMajorMinor",doMajorMinor,arguments);
if(doMajorMinor==0){
fprintf(stderr,"\t-> Must supply -doMajorMinor for calling genotypes\n");
exit(0);
}
if(pest==NULL){
fprintf(stderr,"\t-> You need to supply a sfs as prior (./realSFS output, -pest) to do genotypecalling with saf\n");
exit(0);
}
}
}
double *abcSaf::lbicoTab = NULL;
double **abcSaf::myComb2Tab=NULL;
double *abcSaf::prior = NULL;
abcSaf::abcSaf(const char *outfiles,argStruct *arguments,int inputtype){
theta_res = NULL;
tsktsktsk=0;
tmpChr = NULL;
isHap =0;
//for use when dumping binary indexed saf files
const char *SAF = ".saf.gz";
const char *SAFPOS =".saf.pos.gz";
const char *SAFIDX =".saf.idx";
//for use when dumping binary indexed thetas files
const char *THETAS =".thetas.gz";
const char *THETASIDX =".thetas.idx";
//for use when dumping called genotypes
const char *GENO = ".saf.geno.gz";
//default
underFlowProtect = 0;
fold =0;
isSim =0;
//from command line
anc=NULL;
pest=NULL;
noTrans = 0;
prior = NULL;
doSaf=0;
doPost =0;
doThetas = 0;
outfileSAF = NULL;
outfileSAFPOS = NULL;
outfileSAFIDX = NULL;
theta_dat = NULL;
theta_idx = NULL;
outfileGprobs = NULL;
scalings = NULL;
nnnSites = 0;
if(arguments->argc==2){
if(!strcasecmp(arguments->argv[1],"-doSaf")){
printArg(stdout);
exit(0);
}else
return;
}
getOptions(arguments);
if(doSaf==0){
shouldRun[index] =0;
return;
}
printArg(arguments->argumentFile);
newDim = 2*arguments->nInd+1;
if(fold && isHap){
fprintf(stderr,"\t-> folding for haploid hasn't been defined and implemented\n");
exit(0);
}
if(fold||isHap)
newDim = arguments->nInd+1;
if(doSaf==3){
fprintf(stderr,"\t-> -doSaf 3 Does not work in combination with -snpstat and other snpfilters\n");
outfileGprobs = aio::openFileBG(outfiles,GENO);
}else if(doSaf!=0&&doThetas==0){
outfileSAF = aio::openFileBG(outfiles,SAF);
outfileSAFPOS = aio::openFileBG(outfiles,SAFPOS);
outfileSAFIDX = aio::openFile(outfiles,SAFIDX);
char buf[8]="safv3";
aio::bgzf_write(outfileSAF,buf,8);
aio::bgzf_write(outfileSAFPOS,buf,8);
fwrite(buf,1,8,outfileSAFIDX);
offs[0] = bgzf_tell(outfileSAFPOS);
offs[1] = bgzf_tell(outfileSAF);
size_t tt = newDim-1;
fwrite(&tt,sizeof(tt),1,outfileSAFIDX);
}else {
char buf[8] = "thetav2";
theta_dat = aio::openFileBG(outfiles,THETAS);
theta_idx = aio::openFile(outfiles,THETASIDX);
aio::bgzf_write(theta_dat,buf,8);
fwrite(buf,1,8,theta_idx);
theta_res = new std::vector<float>[5];
offs_thetas = bgzf_tell(theta_dat);
aConst=0;
int nChr = 2*arguments->nInd;
for(int i=1;i<nChr;i++)
aConst += 1.0/i;
aConst = log(aConst);//this is a1
aConst2 = log((nChr*(nChr-1))/2.0);//choose(nChr,2)
aConst3 = log((1.0*nChr-1.0));
scalings = new double [nChr+1];
for(int i=0;i<nChr+1;i++)
scalings[i] = log(i)+log(nChr-i);
if(fold){
for(int i=0;i<newDim-1;i++)// we shouldn't touch the last element
scalings[i] = log(exp(scalings[i]) + exp(scalings[2*arguments->nInd-i]))-log(2.0);//THORFINN NEW
}
}
#if 0//just for printing the scalings
int lim = nChr;
if(fold)
lim = newDim;
for(int i=0;i<newDim;i++)
fprintf(stderr,"SCAL[%d]\t%f\n",i,scalings[i]);
#endif
}
abcSaf::~abcSaf(){
if(doSaf&&doThetas==0&&doSaf!=3)
writeAll();
if(doSaf&&doThetas==1&&doSaf!=3)
writeAllThetas(theta_dat,theta_idx,tmpChr,offs_thetas,theta_pos,theta_res,mynchr);
if(pest) free(pest);
if(prior) delete [] prior;
if(outfileSAF) bgzf_close(outfileSAF);;
if(outfileSAFPOS) bgzf_close(outfileSAFPOS);
if(outfileSAFIDX) fclose(outfileSAFIDX);
if(theta_dat) bgzf_close(theta_dat);
if(theta_idx) fclose(theta_idx);
if(outfileGprobs) bgzf_close(outfileGprobs);
if(lbicoTab) {
delete [] lbicoTab;
}
if(myComb2Tab){
for(int i=0;i<tsktsktsk;i++)
delete [] myComb2Tab[i];
delete [] myComb2Tab;
}
if(tmpChr) free(tmpChr);
if(anc) free(anc);
if(scalings) delete [] scalings;
if(theta_res) delete [] theta_res;
}
void normalize_array(double *d, int len){
double s =0;
for(int i=0;i<len;i++)
s+=d[i];
for(int i=0;i<len;i++)
d[i]=d[i]/s;
}
void normalize_array2(double *d, int len){
double s =0;
for(int i=0;i<len;i++)
s+=exp(d[i]);
s=log(s);
for(int i=0;i<len;i++)
d[i]=d[i]-s;
}
int isSame(double a,double b,double tolerance){
return (fabs(a-b)<tolerance);
}
//18dec 2014 we now condition on the sites where the ancestral is either major or minor.
void filipe::algoJoint(double **liks,char *anc,int nsites,int numInds,int underFlowProtect, int fold,int *keepSites,realRes *r,int noTrans,int doSaf,char *major,char *minor,double *freq,double *indF,int newDim) {
// fprintf(stderr,"liks=%p anc=%p nsites=%d nInd=%d underflowprotect=%d fold=%d keepSites=%p r=%p\n",liks,anc,nsites,numInds,underFlowProtect,fold,keepSites,r);
assert(doSaf==2);
int myCounter =0;
if(anc==NULL||liks==NULL){
fprintf(stderr,"problems receiving data in [%s] will exit (likes=%p||ancestral=%p)\n",__FUNCTION__,liks,anc);
exit(0);
}
double sumMinors[2*numInds+1]; //the sum of the 3 different minors
double m[numInds][3]; //HWE priors
for(int it=0; it<nsites; it++) {//loop over sites
int ancB,derB;
ancB= anc[it];
derB=-1;
if(ancB==4 || keepSites[it]==0){//skip if no ancestral information
keepSites[it] =0; //
continue;
}
//if the ancestral is neither major or the minor skip site
if(ancB!=major[it]&&ancB!=minor[it]){
keepSites[it] =0; //
continue;
}
//set the resultarray to zeros
for(int sm=0 ; sm<(2*numInds+1) ; sm++ ) sumMinors[sm] = 0;
// Assign freqs to ancestral and non-ancestral alleles
double anc_freq, non_anc_freq;
anc_freq = non_anc_freq = freq[it];
if(ancB == major[it]){
anc_freq = 1-freq[it];
derB = minor[it];
}else {
non_anc_freq = 1-freq[it];
derB = major[it];
}
if(noTrans){
if((ancB==2&&derB==0)||(ancB==0&&derB==2))
continue;
if((ancB==1&&derB==3)||(ancB==3&&derB==1))
continue;
}
assert(ancB!=-1&&derB!=-1);
double totmax = 0.0;
int Aa_offset = angsd::majorminor[derB][ancB];//0-9
int AA_offset = angsd::majorminor[derB][derB];//0-9
int aa_offset = angsd::majorminor[ancB][ancB];//0-9
double hj[2*numInds+1];
for(int index=0;index<(2*numInds+1);index++)
if(underFlowProtect==0)
hj[index]=0;
else
hj[index]=log(0);
double PAA,PAa,Paa;
for(int i=0 ; i<numInds ;i++) {
m[i][0] = pow(anc_freq,2.0) + anc_freq*non_anc_freq*indF[i];
m[i][1] = 2.0*anc_freq*non_anc_freq - 2.0*anc_freq*non_anc_freq*indF[i];
m[i][2] = pow(non_anc_freq,2.0) + anc_freq*non_anc_freq*indF[i];
double GAA,GAa,Gaa;
//fix issues where frequency is estimated to zero. Returns very small value
GAA = ((m[i][2] != 0) ? (log(m[i][2])+liks[it][i*10+AA_offset]) : log(DBL_MIN));
GAa = ((m[i][1] != 0) ? (log(m[i][1])+liks[it][i*10+Aa_offset]) : log(DBL_MIN));
Gaa = ((m[i][0] != 0) ? (log(m[i][0])+liks[it][i*10+aa_offset]) : log(DBL_MIN));
double mymax;
if (Gaa > GAa && Gaa > GAA) mymax = Gaa;
else if (GAa > GAA) mymax = GAa;
else mymax = GAA;
if(mymax<MINLIKE){
Gaa = 0;
GAa = 0;
GAA = 0;
totmax = totmax + mymax;
}else{
Gaa=Gaa-mymax;
GAa=GAa-mymax;
GAA=GAA-mymax;
totmax = totmax + mymax;
}
if(underFlowProtect==0){
PAA=exp(GAA);
PAa=exp(GAa);
Paa=exp(Gaa);
}else{
PAA =(GAA);
PAa =(GAa);
Paa =(Gaa);
}
if(std::isnan(Paa)||std::isnan(PAa)||std::isnan(Paa))
fprintf(stderr,"Possible underflow PAA=%f\tPAa=%f\tPaa=%f\n",PAA,PAa,Paa);
if(i==0){
hj[0] =Paa;
hj[1] =PAa;
hj[2] =PAA;
}else{
for(int j=2*(i+1); j>1;j--){
double tmp;
if(underFlowProtect==1)
tmp = angsd::addProtect3(log(m[i][2])+PAA+hj[j-2],log(m[i][1])+PAa+hj[j-1],log(m[i][0])+Paa+hj[j]);
else
tmp = m[i][2]*PAA*hj[j-2] + m[i][1]*PAa*hj[j-1] + m[i][0]*Paa*hj[j];
if(std::isnan(tmp)){
fprintf(stderr,"is nan:%d\n",j );
hj[j] = 0;
break;
}else
hj[j] = tmp;
}
if(underFlowProtect==1){
hj[1] = angsd::addProtect2(log(m[i][0])+Paa+hj[1],log(m[i][1])+PAa+hj[0]);
hj[0] = log(m[i][0]) + Paa + hj[0];
}
else{
hj[1] = m[i][0]*Paa*hj[1] + m[i][1]*PAa*hj[0];
hj[0] = m[i][0]*Paa*hj[0];
}
}
}
for(int i=0;i<(2*numInds+1);i++)
if(underFlowProtect==0){
sumMinors[i] += hj[i];
// sumMinors[i] += hj[i]/(1-hj[0]-hj[2*numInds]); //As in the PLoS ONE paper
}else{
sumMinors[i] = exp(angsd::addProtect2(log(sumMinors[i]),hj[i]));
//sumMinors[i] =
// exp(angsd::addProtect2(log(sumMinors[i]),hj[i]-log(1-hj[0]-hj[2*numInds])));
//As in the PLoS ONE paper
}
//sumMinors is in normal space, not log
/*
we do 3 things.
1. log scaling everyting
2. rescaling to the most likely in order to avoid underflows in the optimization
3. we might do a fold also.
*/
if(fold) {
//newDim is set in constructor
for(int i=0;i<newDim-1;i++)// we shouldn't touch the last element
sumMinors[i] = log(sumMinors[i] + sumMinors[2*numInds-i]);
sumMinors[newDim-1] = log(sumMinors[newDim-1])+log(2.0);
//angsd::logrescale(sumMinors,newDim);
double ts=0;
for(int i=0;i<newDim;i++)
ts += exp(sumMinors[i]);
ts = log(ts);
for(int i=0;i<newDim;i++)
sumMinors[i] = sumMinors[i]-ts;
if(std::isnan(sumMinors[0]))
r->oklist[it] = 2;
else{
r->oklist[it] = 1;
r->pLikes[myCounter] =new float[numInds+1];
for(int iii=0;iii<numInds+1;iii++)
r->pLikes[myCounter][iii] = sumMinors[iii];
// memcpy(r->pLikes[myCounter],sumMinors,sizeof(double)*(numInds+1));
myCounter++;
}
}else{
for(int i=0;i<2*numInds+1;i++)
sumMinors[i] = log(sumMinors[i]);
// angsd::logrescale(sumMinors,2*numInds+1);
double ts=0;
for(int i=0;i<newDim;i++)
ts += exp(sumMinors[i]);
ts = log(ts);
for(int i=0;i<newDim;i++)
sumMinors[i] = sumMinors[i]-ts;
if(std::isnan(sumMinors[0]))
r->oklist[it] = 2;
else{
r->oklist[it] = 1;
r->pLikes[myCounter] =new float[2*numInds+1];
for(int iii=0;iii<2*numInds+1;iii++)
r->pLikes[myCounter][iii] = sumMinors[iii];
// memcpy(r->pLikes[myCounter],sumMinors,sizeof(double)*(2*numInds+1));
myCounter++;
}
}
}
}
void abcSaf::algoJointPost(double **post,int nSites,int nInd,int *keepSites,realRes *r,int doFold){
// fprintf(stderr,"[%s] nsites:%d r:%p r->pLikes:%p\n",__FUNCTION__,nSites,r,r->pLikes);
int myCounter =0;
for(int s=0;s<nSites;s++){
if(keepSites[s]==0)
continue;
double *liks=post[s]; //we call this liks, eventhough it is posteriors.
double *hj = new double [2*nInd+1];
for(int index=0;index<(2*nInd+1);index++)
hj[index]=0;
//initalize
memcpy(hj,liks,3*sizeof(double));
for(int i=1 ; i<nInd ;i++) {
double Paa=liks[i*3];
double PAa=2*liks[i*3+1];
double PAA=liks[i*3+2];
for(int j=2*(i+1); j>1;j--)
hj[j] = PAA*hj[j-2]+PAa*hj[j-1]+Paa*hj[j];
hj[1] = Paa*hj[1] + PAa*hj[0];
hj[0] = Paa*hj[0];
normalize_array(hj,2*(i+1));
}
for(int i=0;i<(2*nInd+1);i++)
hj[i] = log(hj[i])-lbicoTab[i];
if(doFold){
for(int i=0;i<newDim-1;i++)// we shouldn't touch the last element
hj[i] = log(exp(hj[i]) + exp(hj[2*nInd-i]));
hj[newDim-1] = hj[newDim-1]+log(2.0);
}
angsd::logrescale(hj,2*nInd+1);
if(std::isnan(hj[0]))
r->oklist[s] = 2;
else{
r->oklist[s] = 1;
r->pLikes[myCounter]= new float[2*nInd+1];
for(int iii=0;iii<2*nInd+1;iii++)
r->pLikes[myCounter][iii] = hj[iii];
myCounter++;
}
}
}
//AA,AC,AG,AT,CC,CG,CT,GG,GT,TT
int homo[4] = {0,4,7,9};
void abcSaf::algoJointHap(double **liks,char *anc,int nsites,int numInds,int underFlowProtect, int fold,int *keepSites,realRes *r,int noTrans) {
int myCounter =0;
if(anc==NULL||liks==NULL){
fprintf(stderr,"problems receiving data in [%s] will exit (likes=%p||ancestral=%p)\n",__FUNCTION__,liks,anc);
exit(0);
}
double sumMinors[numInds+1]; //the sum of the 3 different minors
for(int it=0; it<nsites; it++) {//loop over sites
int major_offset = anc[it];
if(major_offset==4||(keepSites[it]==0)){//skip of no ancestral information
keepSites[it] =0; //
// r->oklist is zero no need to update
continue;
}
//set the resultarray to zeros
for(int sm=0 ; sm<numInds+1 ; sm++ )
sumMinors[sm] = 0;
//loop through the 3 different minors
for(int minor_offset=0;minor_offset<4;minor_offset++) {
if(minor_offset == major_offset)
continue;
if(noTrans){
if((major_offset==2&&minor_offset==0)||(major_offset==0&&minor_offset==2))
continue;
if((major_offset==1&&minor_offset==3)||(major_offset==3&&minor_offset==1))
continue;
}
double totmax = 0.0;
//hook for only calculating one minor
// int Aa_offset = angsd::majorminor[minor_offset][major_offset];//0-9
int AA_offset = homo[major_offset];//angsd::majorminor[minor_offset][minor_offset];//0-9
int aa_offset = homo[minor_offset];//angsd::majorminor[major_offset][major_offset];//0-9
// fprintf(stderr,"%d:%d\t%d\t%d\n",major_offset,Aa_offset,AA_offset,aa_offset);
//part two
double hj[numInds+1];
for(int index=0;index<(2*numInds+1);index++)
if(underFlowProtect==0)
hj[index]=0;
else
hj[index]=log(0);
double PAA,Paa;
for(int i=0 ; i<numInds ;i++) {
double GAA,Gaa;
GAA = liks[it][i*10+AA_offset];
Gaa = liks[it][i*10+aa_offset];
//do underlfow protection (we are in logspace here) (rasmus style)
if(1){
double mymax=std::max(Gaa,GAA);
// fprintf(stdout,"mymax[%d]=%f\t",i,mymax);
if(mymax<MINLIKE){
// fprintf(stderr,"\n%f %f %f\n",GAA, GAa,Gaa);
Gaa = 0;
GAA = 0;
totmax = totmax + mymax;
}else{
Gaa=Gaa-mymax;
GAA=GAA-mymax;
totmax = totmax + mymax;
}
// fprintf(stderr,"totmax=%f\n",totmax);
//END underlfow protection (we are in logspace here) (rasmus style)
}
if(underFlowProtect==0){
PAA=exp(GAA);
Paa=exp(Gaa);
}else{
PAA =(GAA);///(MAA+MAa+Maa);
Paa =(Gaa);///(MAA+MAa+Maa);
}
//check for underflow error, this should only occur once in a blue moon
if(std::isnan(Paa)||std::isnan(PAA)){
fprintf(stderr,"PAA=%f\tPaa=%f\n",PAA,Paa);
}
// fprintf(stdout,"it=%d PAA=%f\tPAa=%f\tPaa=%f\n",it,PAA,PAa,Paa);
if(i==0){
hj[0] =Paa;
hj[1] =PAA;
}else{
//fprintf(stderr,"asdf\n");
for(int j=i+1; j>0;j--) {
double tmp;
if(underFlowProtect==1)
tmp =angsd::addProtect2(PAA+hj[j-1],Paa+hj[j]);
else
tmp = PAA*hj[j-1]+Paa*hj[j];
if(std::isnan(tmp)){
fprintf(stderr,"is nan:%d\n",j );
hj[j] = 0;
break;
}else
hj[j] =tmp;
}
if(underFlowProtect==1)
hj[0] = Paa+hj[0];
else
hj[0] = Paa*hj[0];
}
//ifunderflowprotect then hj is in logspace
}
for(int i=0;i<numInds+1;i++)
if(underFlowProtect==0)
sumMinors[i] += exp(log(hj[i])-lbicoTab[i]+totmax);
else
sumMinors[i] = exp(angsd::addProtect2(log(sumMinors[i]),hj[i]-lbicoTab[i]+totmax));
}
//sumMinors is in normal space, not log
/*
we do 3 things.
1. log scaling everyting
2. rescaling to the most likely in order to avoid underflows in the optimization
3. we might do a fold also.
*/
{
for(int i=0;i<numInds+1;i++)
sumMinors[i] = log(sumMinors[i]);
angsd::logrescale(sumMinors,numInds+1);
if(std::isnan(sumMinors[0]))
r->oklist[it] = 2;
else{
r->oklist[it] = 1;
r->pLikes[myCounter] =new float[numInds+1];
for(int iii=0;iii<numInds+1;iii++)
r->pLikes[myCounter][iii] = sumMinors[iii];
// memcpy(r->pLikes[myCounter],sumMinors,sizeof(double)*(numInds+1));
myCounter++;
}
}
}
}
void abcSaf::algoJoint(double **liks,char *anc,int nsites,int numInds,int underFlowProtect, int fold,int *keepSites,realRes *r,int noTrans) {
// fprintf(stderr,"[%s]\n",__FUNCTION__);
int myCounter =0;
if(anc==NULL||liks==NULL){
fprintf(stderr,"problems receiving data in [%s] will exit (likes=%p||ancestral=%p)\n",__FUNCTION__,liks,anc);
exit(0);
}
double sumMinors[2*numInds+1]; //the sum of the 3 different minors
for(int it=0; it<nsites; it++) {//loop over sites
int major_offset = anc[it];
//fprintf(stderr,"anc[it]:%d\n",anc[it]);
if(major_offset==4||(keepSites[it]==0)){//skip of no ancestral information
keepSites[it] =0; //
// r->oklist is zero no need to update
continue;
}
// fprintf(stderr,"hello im here\n");
//set the resultarray to zeros
for(int sm=0 ; sm<(2*numInds+1) ; sm++ )
sumMinors[sm] = 0;
//loop through the 3 different minors
for(int minor_offset=0;minor_offset<4;minor_offset++) {
if(minor_offset == major_offset)
continue;
if(noTrans){
if((major_offset==2&&minor_offset==0)||(major_offset==0&&minor_offset==2))
continue;
if((major_offset==1&&minor_offset==3)||(major_offset==3&&minor_offset==1))
continue;
}
double totmax = 0.0;
//hook for only calculating one minor
int Aa_offset = angsd::majorminor[minor_offset][major_offset];//0-9
int AA_offset = angsd::majorminor[minor_offset][minor_offset];//0-9
int aa_offset = angsd::majorminor[major_offset][major_offset];//0-9
// fprintf(stderr,"%d:%d\t%d\t%d\n",major_offset,Aa_offset,AA_offset,aa_offset);
//part two
double hj[2*numInds+1];
for(int index=0;index<(2*numInds+1);index++)
if(underFlowProtect==0)
hj[index]=0;
else
hj[index]=log(0);
double PAA,PAa,Paa;
for(int i=0 ; i<numInds ;i++) {
// printf("pre scale AA=%f\tAa=%f\taa=%f\n",liks[it][i*3+AA_offset],liks[it][i*3+Aa_offset],liks[it][i*3+aa_offset]);
double GAA,GAa,Gaa;
#ifdef RESCALE
if(0){//The rescaling is now done in 'getMajorMinor()'
double max = liks[it][i*10+0];
for(int index=1;index<10;index++)
if(liks[it][i*10+index]>max)
max = liks[it][i*10+index];
for(int index=0;index<10;index++)
liks[it][i*10+index] = liks[it][i*10+index]-max;
}
#endif
//printf("post scale AA=%f\tAa=%f\taa=%f\n",liks[it][i*3+AA_offset],liks[it][i*3+Aa_offset],liks[it][i*3+aa_offset]);
GAA = liks[it][i*10+AA_offset];
GAa = log(2.0)+liks[it][i*10+Aa_offset];
Gaa = liks[it][i*10+aa_offset];
//printf("[GAA] GAA=%f\tGAa=%f\tGaa=%f\n",GAA,GAa,Gaa);
//do underlfow protection (we are in logspace here) (rasmus style)
if(1){
double mymax;
if (Gaa > GAa && Gaa > GAA) mymax = Gaa;
else if (GAa > GAA) mymax = GAa;
else mymax = GAA;
// fprintf(stdout,"mymax[%d]=%f\t",i,mymax);
if(mymax<MINLIKE){
// fprintf(stderr,"\n%f %f %f\n",GAA, GAa,Gaa);
Gaa = 0;
GAa = 0;
GAA = 0;
totmax = totmax + mymax;
}else{
Gaa=Gaa-mymax;
GAa=GAa-mymax;
GAA=GAA-mymax;
totmax = totmax + mymax;
}
// fprintf(stderr,"totmax=%f\n",totmax);
//END underlfow protection (we are in logspace here) (rasmus style)
}
if(underFlowProtect==0){
PAA=exp(GAA);
PAa=exp(GAa);
Paa=exp(Gaa);
}else{
PAA =(GAA);///(MAA+MAa+Maa);
PAa =(GAa);///(MAA+MAa+Maa);
Paa =(Gaa);///(MAA+MAa+Maa);
}
//check for underflow error, this should only occur once in a blue moon
if(std::isnan(Paa)||std::isnan(PAa)||std::isnan(Paa)){
fprintf(stderr,"PAA=%f\tPAa=%f\tPaa=%f\n",PAA,PAa,Paa);
}
// fprintf(stdout,"it=%d PAA=%f\tPAa=%f\tPaa=%f\n",it,PAA,PAa,Paa);
if(i==0){
hj[0] =Paa;
hj[1] =PAa;
hj[2] =PAA;
}else{
//fprintf(stderr,"asdf\n");
for(int j=2*(i+1); j>1;j--){
// print_array(stdout,hj,2*numInds+1,0);
//print_array(hj,2*numInds+1);
double tmp;
if(underFlowProtect==1)
tmp =angsd::addProtect3(PAA+hj[j-2],PAa+hj[j-1],Paa+hj[j]);
else
tmp = PAA*hj[j-2]+PAa*hj[j-1]+Paa*hj[j];
if(std::isnan(tmp)){
fprintf(stderr,"is nan:%d\n",j );
hj[j] = 0;
break;
}else
hj[j] =tmp;
}
if(underFlowProtect==1){
hj[1] = angsd::addProtect2(Paa+hj[1],PAa+hj[0]);
hj[0] = Paa+hj[0];
}
else{
hj[1] = Paa*hj[1] + PAa*hj[0];
hj[0] = Paa*hj[0];
}
}
//ifunderflowprotect then hj is in logspace
}
// fprintf(stderr,"%f %f %f\n",hj[0],hj[1],hj[2]);
//fprintf(stdout,"\nscaledLikes=");
for(int ii=0;0&&ii<10*numInds;ii++)
fprintf(stdout,"%f\t",liks[it][ii]);
// totmax=0;
for(int i=0;i<(2*numInds+1);i++)
if(underFlowProtect==0)
sumMinors[i] += exp(log(hj[i])-lbicoTab[i]+totmax);
else
sumMinors[i] = exp(angsd::addProtect2(log(sumMinors[i]),hj[i]-lbicoTab[i]+totmax));
}
//sumMinors is in normal space, not log
/*
we do 3 things.
1. log scaling everyting
2. rescaling to the most likely in order to avoid underflows in the optimization
3. we might do a fold also.
*/
if(fold) {
int newDim = numInds+1;
for(int i=0;i<newDim-1;i++)// we shouldn't touch the last element
sumMinors[i] = log(sumMinors[i] + sumMinors[2*numInds-i]);//THORFINN NEW
sumMinors[newDim-1] = log(sumMinors[newDim-1])+log(2.0);
angsd::logrescale(sumMinors,newDim);
if(std::isnan(sumMinors[0]))
r->oklist[it] = 2;
else{
r->oklist[it] = 1;
r->pLikes[myCounter] =new float[numInds+1];
for(int iii=0;iii<numInds+1;iii++)
r->pLikes[myCounter][iii] = sumMinors[iii];
//memcpy(r->pLikes[myCounter],sumMinors,sizeof(double)*(numInds+1));
myCounter++;
}
}else{
for(int i=0;i<2*numInds+1;i++)
sumMinors[i] = log(sumMinors[i]);
angsd::logrescale(sumMinors,2*numInds+1);
// fprintf(stderr,"sumMinors[0]:%f\n",sumMinors[0]);
if(std::isnan(sumMinors[0]))
r->oklist[it] = 2;
else{
r->oklist[it] = 1;
r->pLikes[myCounter] =new float[2*numInds+1];
for(int iii=0;iii<2*numInds+1;iii++){
// fprintf(stderr,"iii:%f\n",sumMinors[iii]);
r->pLikes[myCounter][iii] = sumMinors[iii];
}
// memcpy(r->pLikes[myCounter],sumMinors,sizeof(double)*(2*numInds+1));
myCounter++;
}
}
}