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abcSaf.cpp
1851 lines (1551 loc) · 51.1 KB
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abcSaf.cpp
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#include <cstdio>
#include <cmath>
#include <cfloat>
#include <htslib/kstring.h>
#include "abcFreq.h"
#include "shared.h"
#include "analysisFunction.h"
#include <pthread.h>
#include "abc.h"
#include "abcSaf.h"
#include "aio.h"
#include <limits>
#include <iostream>
#define MINLIKE -1000.0 //this is for setting genotypelikelhoods to missing (EXPLAINED BELOW)
const double NEG_INF = -std::numeric_limits<double>::infinity();
int homo[4] = {0,4,7,9}; //AA,AC,AG,AT,CC,CG,CT,GG,GT,TT
namespace filipe{
void algoJoint(double **liks,char *anc,int nsites,int numInds,int underFlowProtect, 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,"\t 1: SAF calculation integrating over possible minor alleles\n\t 2: SAF calculation incorporating inbreeding\n\t 3: Calculate genotype probabilities using SAF (DEPRECATED; use -doPost 3)\n\t 4: SAF calculation from genotype posteriors (input is beagle text format)\n\t 5: SAF calculation conditioning on minor allele from -doMajorMinor\n");
fprintf(argFile,"\t -underFlowProtect\t%d\n",underFlowProtect);
fprintf(argFile,"\t -anc\t\t%s\t(ancestral fasta)\n",anc);
fprintf(argFile,"\t -noTrans\t%d\t(remove transitions)\n",noTrans);
fprintf(argFile,"\t -pest\t\t%s\t(prior SFS)\n",pest);
fprintf(argFile,"\t -isHap\t\t%d\t(samples are haploid; works with -doSaf 1 or 5)\n",isHap);
fprintf(argFile,"\t -scoreTol\t%.1e\t(tolerance for score-limited algorithm)\n",scoreTol);
fprintf(argFile,"\t -doPost\t%d\t(doPost 3, used for accessing SAF based variables)\n",doPost);
fprintf(argFile,"\nNB: If -pest is supplied in addition to -doSaf then the output will be posterior probabilities of the sample allele frequency for each site\n");
fprintf(argFile,"NB: Increasing -scoreTol will trade accuracy for reduced computation time and storage\n");
}
void abcSaf::getOptions(argStruct *arguments){
doSaf = angsd::getArg("-doSaf",doSaf,arguments);
doPost = angsd::getArg("-doPost",doPost,arguments);
isHap = angsd::getArg("-isHap",isHap,arguments);
isSim = angsd::getArg("-isSim",isSim,arguments);
pest = angsd::getArg("-pest",pest,arguments);
minInd = angsd::getArg("-minInd",minInd,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){
prior=angsd::readDouble(pest,arguments->nInd*2+1);
int nd=arguments->nInd*2+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;
}
scoreTol = angsd::getArg("-scoreTol",scoreTol,arguments);
noTrans = angsd::getArg("-noTrans",noTrans,arguments);
int GL = 0;
GL = angsd::getArg("-GL",GL,arguments);
int doPost = 0;
doPost = angsd::getArg("-doPost",doPost,arguments);
if(doSaf==0&&doPost!=3)
return;
underFlowProtect=angsd::getArg("-underFlowProtect",underFlowProtect,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(doSaf !=4){
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==4){
if(doPost==0 && ai!=INPUT_VCF_GP){
fprintf(stderr,"\t-> You have requested to do SAF estimation from genotype posteriors (GP), either use input file that contains GP or compute -doPost\n");
}else
fprintf(stderr,"\t-> You have requested to do SAF estimation from genotype posteriors, this has not been tested fully\n");
}
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 5\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){
tsktsktsk = 0;
tmpChr = NULL;
isHap = 0;
sumBand = 0;
minInd=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 called genotypes
const char *GENO = ".saf.geno.gz";
//default
underFlowProtect = 0;
isSim =0;
//from command line
anc = NULL;
pest = NULL;
noTrans = 0;
prior = NULL;
doSaf = 0;
doPost = 0;
outfileSAF = NULL;
outfileSAFPOS = NULL;
outfileSAFIDX = NULL;
outfileGprobs = NULL;
nnnSites = 0;
scoreTol = 1.e-9;
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(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){
outfileSAF = aio::openFileBG(outfiles,SAF);
outfileSAFPOS = aio::openFileBG(outfiles,SAFPOS);
outfileSAFIDX = aio::openFile(outfiles,SAFIDX);
char buf[8]="safv4";
aio::bgzf_write(outfileSAF,buf,8);
aio::bgzf_write(outfileSAFPOS,buf,8);
fwrite(buf,1,8,outfileSAFIDX);
aio::doAssert(bgzf_flush(outfileSAF)==0);aio::doAssert(bgzf_flush(outfileSAFPOS)==0);
offs[0] = bgzf_tell(outfileSAFPOS);
offs[1] = bgzf_tell(outfileSAF);
size_t tt = newDim-1;
fwrite(&tt,sizeof(tt),1,outfileSAFIDX);
}
}
abcSaf::~abcSaf(){
if(doSaf&&doSaf!=3)
writeAll();
if(pest) free(pest);
if(prior) delete [] prior;
if(outfileSAF) bgzf_close(outfileSAF);;
if(outfileSAFPOS) bgzf_close(outfileSAFPOS);
if(outfileSAFIDX) fclose(outfileSAFIDX);
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);
}
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);
}
// --- banded SAF algorithm adapted from Han & Novembre 2015 Bioinformatics --- //
double logSumExp (double a, double b)
{
// b/c angsd::addProtect2 farts out when both terms are -Inf
double mx = a > b ? a : b;
if (std::isinf(mx)) mx = 0.;
a = exp(a - mx);
b = exp(b - mx);
return log(a + b) + mx;
}
double saf_like_hap (double *p, double *h, int N, int j)
{
double tmp;
tmp = 0.;
if(j >= 0 && j < N)
tmp += (N-j)*p[0]*h[j];
if(j-1 >= 0)
tmp += j*p[1]*h[j-1];
if(std::isnan(tmp))
{
fprintf(stderr, "is nan: %d\n", j);
tmp = 0.;
}
return tmp;
}
void banded_saf_algo_hap (double* hj, int& lower, int& upper, double* p, const int i, const int numChr, const double tol)
{
int mle = p[0] > p[1] ? 0 : 1; //missing: 1
lower += mle;
upper += mle;
while (true)
{
if (lower == 0 || saf_like_hap(p, hj, numChr, lower) < tol)
break;
lower -= 1;
}
while (true)
{
if (upper == numChr || saf_like_hap(p, hj, numChr, upper) < tol)
break;
upper += 1;
}
for (int j=upper; j>=lower; --j)
hj[j] = saf_like_hap (p, hj, numChr, j);
}
void saf_algo_hap (double* hj, int& lower, int& upper, double& sm, double& score_tol, double* p, const int i, const int numChr)
{
int lower_old = lower,
upper_old = upper;
banded_saf_algo_hap(hj, lower, upper, p, i, numChr, score_tol);
// normalize
double den = 0.;
for (int j=lower; j<=upper; ++j)
if (hj[j] > den)
den = hj[j];
for (int j=lower; j<=upper; ++j)
hj[j] /= den;
// clean up edges
for (int j=lower_old; j<lower; ++j)
hj[j] = 0.;
for (int j=upper_old; j>upper; --j)
hj[j] = 0.;
// track normalizing constant
sm += log(den);
}
double saf_like_dip (double *p, double *h, int N, int j)
{
double tmp;
tmp = 0.;
if(j >= 0 && j < N)
tmp += (N-j)*(N-j-1)*p[0]*h[j];
if(j-1 >= 0 && j < N)
tmp += 2*j*(N-j)*p[1]*h[j-1];
if(j-2 >= 0 && j <= N)
tmp += j*(j-1)*p[2]*h[j-2];
if(std::isnan(tmp))
{
fprintf(stderr, "is nan: %d\n", j);
tmp = 0.;
}
return tmp;
}
void vanilla_saf_algo_dip (double* hj, int& lower, int& upper, double* p, const int i, const int numChr, const double tol)
{
lower = 0;
upper = 2*(i+1);
for(int j=upper; j>=lower; j--)
hj[j] = saf_like_dip(p, hj, numChr, j);
}
void banded_saf_algo_dip (double* hj, int& lower, int& upper, double* p, const int i, const int numChr, const double tol)
{
int mle = (p[0] > p[1] && p[0] > p[2]) ? 0 : (p[1] > p[2] ? 1 : 2); //missing: 2
lower += mle;
upper += mle;
while (true)
{
if (lower == 0 || saf_like_dip(p, hj, numChr, lower) < tol)
break;
lower -= 1;
}
while (true)
{
if (upper == numChr || saf_like_dip(p, hj, numChr, upper) < tol)
break;
upper += 1;
}
for (int j=upper; j>=lower; --j)
hj[j] = saf_like_dip (p, hj, numChr, j);
}
void saf_algo_dip (double* hj, int& lower, int& upper, double& sm, double& score_tol, double* p, const int i, const int numChr)
{
int lower_old = lower,
upper_old = upper;
if (p[1] < p[0] && p[1] < p[2]) // ... then update may not be unimodal, should pass over all bins
score_tol = 0.; //this will force all future updates for this site to pass over all bins
if (score_tol > 0.)
banded_saf_algo_dip(hj, lower, upper, p, i, numChr, score_tol);
else
vanilla_saf_algo_dip(hj, lower, upper, p, i, numChr, score_tol);
// normalize
double den = 0.;
for (int j=lower; j<=upper; ++j)
if (hj[j] > den)
den = hj[j];
for (int j=lower; j<=upper; ++j)
hj[j] /= den;
// clean up edges
for (int j=lower_old; j<lower; ++j)
hj[j] = 0.;
for (int j=upper_old; j>upper; --j)
hj[j] = 0.;
// track normalizing constant
sm += log(den);
}
int saf_sparsify_and_normalize (double* hj, int& lower, int& upper, const double tol)
{
// rescale in logspace
double mx = NEG_INF;
for (int j=lower; j<=upper; ++j)
if (hj[j] > mx)
mx = hj[j];
for (int j=lower; j<=upper; ++j)
hj[j] -= mx;
// another pass to thin band
bool big_enough;
int lower0 = lower,
upper0 = upper;
lower = upper0;
upper = lower0;
for (int j=lower0; j<=upper0; ++j)
{
big_enough = hj[j] >= log(tol);
if (big_enough && j > upper)
upper = j;
if (big_enough && j < lower)
lower = j;
}
if (lower == upper0 || upper == lower0)
{ // unlikely, but could happen if there's underflow
lower = lower0;
upper = upper0;
// fprintf(stderr, "\t-> Banding failed\n");
return 1;
}
return 0;
}
// --- different options for -doSaf --- //
// NSP 3July2020
// I did not implement banded/score-limited algo for this.
// However, I think there is a bug here -- the prior gets multiplied into the genotype likelihoods twice.
// I would not trust the output of this method until this gets investigated.
void filipe::algoJoint(double **liks,char *anc,int nsites,int numInds,int underFlowProtect, 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);
aio::doAssert(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;
}
aio::doAssert(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.
*/
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 now, to make this safv4
r->pBound[myCounter] = new int[2];
r->pBound[myCounter][0] = 0;
r->pBound[myCounter][1] = 2*numInds+1;
// \for now
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 counter = 0;
int numChr = nInd*2;
for(int s=0; s<nSites; s++)
{
if(keepSites[s]==0)
continue;
double *liks = post[s]; //we call this liks, even though it is posteriors.
double hj[numChr+1];
for(int i=0; i<numChr+1; i++)
hj[i] = 0;
double tmx = 0.;
//initialize
for (int i=0; i<nInd*3; ++i)
{
if(liks[i] < 0.0)
{
fprintf(stderr, "Negative genotype probability in %s will exit (site=%d,ind=%d,lik=%f)\n", __FUNCTION__, s, i, liks[i]);
exit(0);
}
}
memcpy(hj, liks, 3*sizeof(double));
int lower = 0,
upper = 2;
double score_tol = scoreTol;
double p[3];
for(int i=1; i<nInd; i++)
{
p[0] = liks[i*3];
p[1] = liks[i*3+1];
p[2] = liks[i*3+2];
saf_algo_dip(hj, lower, upper, tmx, score_tol, p, i, 2*(i+1));
}
for(int j=lower; j<=upper; j++)
hj[j] = log(hj[j]) + tmx;
if(saf_sparsify_and_normalize (hj, lower, upper, scoreTol))
r->oklist[s] = 3;
if(std::isnan(hj[lower]))
r->oklist[s] = 2;
else
{
r->oklist[s] = 1;
r->pLikes[counter] = new float[upper - lower + 1];
r->pBound[counter] = new int[2];
int k=0;
for(int j=lower; j<=upper; j++)
r->pLikes[counter][k++] = hj[j];
r->pBound[counter][0] = lower;
r->pBound[counter][1] = upper - lower + 1;
////debug
//fprintf(stdout, "%u\t%u\t%u", counter, lower, upper-lower+1);
//k=0;
//for(int j=lower; j<=upper; ++j)
// fprintf(stdout, "\t%f", r->pLikes[counter][k++]);
//fprintf(stdout, "\n");
counter++;
}
}
}
void abcSaf::algoJointHap(double **liks,
char *anc,int nsites,
int numInds,
int *keepSites,
realRes *r,
int noTrans)
{
int counter = 0;
int numChr = numInds;
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[numChr+1];
for(int it=0; it<nsites; it++)
{
int major_offset = anc[it];
if(major_offset==4 || keepSites[it]==0)
{ //skip if no ancestral information
keepSites[it] = 0;
continue;
}
for(int j=0; j<numChr+1; j++)
sumMinors[j] = NEG_INF;
int lower_all = numChr,
upper_all = 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 tmx = 0.;
int AA_offset = homo[major_offset];
int aa_offset = homo[minor_offset];
double p[2];
double score_tol = scoreTol;
double hj[numChr+1];
for(int j=0; j<numChr+1; j++) hj[j] = 0.;
int lower = 0,
upper = 1;
for(int i=0; i<numInds; i++)
{
p[0] = liks[it][i*10+AA_offset];
p[1] = liks[it][i*10+aa_offset];
//underflow protection
double mx = p[1] > p[0] ? p[1] : p[0];
tmx += mx;
p[0] = mx < MINLIKE ? 1. : exp(p[0] - mx);
p[1] = mx < MINLIKE ? 1. : exp(p[1] - mx);
//check for underflow error, this should only occur once in a blue moon
if(std::isnan(p[0])||std::isnan(p[1]))
fprintf(stderr,"PAA=%f\tPaa=%f\n",p[1],p[0]);
if(i==0)
{
hj[0] = p[0];
hj[1] = p[1];
}
else
saf_algo_hap(hj, lower, upper, tmx, score_tol, p, i, i+1);
}
for(int j=lower; j<=upper; j++)
sumMinors[j] = logSumExp(sumMinors[j], log(hj[j])+tmx);
if (lower < lower_all)
lower_all = lower;
if (upper > upper_all)
upper_all = upper;
}
if(saf_sparsify_and_normalize (sumMinors, lower_all, upper_all, scoreTol))
r->oklist[it] = 3;
if(std::isnan(sumMinors[lower_all]))
r->oklist[it] = 2;
else
{
r->oklist[it] = 1;
r->pLikes[counter] = new float[upper_all-lower_all+1];
r->pBound[counter] = new int[2];
int k = 0;
for(int j=lower_all; j<=upper_all; ++j)
r->pLikes[counter][k++] = sumMinors[j];
r->pBound[counter][0] = lower_all;
r->pBound[counter][1] = upper_all-lower_all+1;
////debug
//fprintf(stdout, "%u\t%u\t%u", counter, lower_all, upper_all-lower_all+1);
//k=0;
//for(int j=lower_all; j<=upper_all; ++j)
// fprintf(stdout, "\t%f", r->pLikes[counter][k++]);
//fprintf(stdout, "\n");
counter++;
}
}
}
void abcSaf::algoJoint(double **liks,
char *anc,
int nsites,
int numInds,
int *keepSites,
realRes *r,
int noTrans)
{
int counter = 0;
int numChr = 2*numInds;
if(anc==NULL||liks==NULL)
{
fprintf(stderr, "\t-> problems receiving data in [%s] will exit (likes=%p||ancestral=%p)\n", __FUNCTION__, liks, anc);
exit(0);
}
double sumMinors[numChr+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 if no ancestral information
keepSites[it] = 0;
continue;
}
{ //check that fixing the ancestral produces meaningful results (anc is not major or minor)
//AA,AC,AG,AT,CC,CG,CT,GG,GT,TT
double glsum[4] = {0,0,0,0};
for(int ss=0; ss<numInds; ss++){
glsum[0] += liks[it][10*ss];
glsum[1] += liks[it][10*ss+4];
glsum[2] += liks[it][10*ss+7];
glsum[3] += liks[it][10*ss+9];
}
int howmanysmaller = 0;
for(int i=0; i<4; i++){
//fprintf(stderr,"anc: %d gl[%d]: %f\n",anc[it],i,glsum[i]);
if(glsum[i]<=glsum[anc[it]])
howmanysmaller++;
}
if(0&&howmanysmaller==2)
continue;
//fprintf(stderr,"How many smaller: %d\n",howmanysmaller);
}
for(int j=0; j<numChr+1; j++)
sumMinors[j] = NEG_INF;
int lower_all = numChr,
upper_all = 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 tmx = 0.; //denominator in logspace
int Aa_offset = angsd::majorminor[minor_offset][major_offset];
int AA_offset = angsd::majorminor[minor_offset][minor_offset];
int aa_offset = angsd::majorminor[major_offset][major_offset];
double p[3];
double score_tol = scoreTol;
double hj[numChr+1];
for(int j=0; j<numChr+1; j++) hj[j] = 0.;
int lower = 0,
upper = 2;
for(int i=0; i<numInds; i++)
{
p[0] = liks[it][i*10+aa_offset];
p[1] = liks[it][i*10+Aa_offset];
p[2] = liks[it][i*10+AA_offset];
//underflow protection
double mx;
if (p[2] > p[1] && p[2] > p[0]) mx = p[2];
else if (p[1] > p[0]) mx = p[1];
else mx = p[0];
tmx += mx;
p[0] = mx < MINLIKE ? 1. : exp(p[0] - mx);
p[1] = mx < MINLIKE ? 1. : exp(p[1] - mx);
p[2] = mx < MINLIKE ? 1. : exp(p[2] - mx);
//check for underflow error, this should only occur once in a blue moon
if(std::isnan(p[0])||std::isnan(p[1])||std::isnan(p[2]))
fprintf(stderr,"PAA=%f\tPAa=%f\tPaa=%f\n",p[2],p[1],p[0]);
if(i==0)
{
hj[0] = p[0];
hj[1] = p[1];
hj[2] = p[2];
}
else
{
saf_algo_dip(hj, lower, upper, tmx, score_tol, p, i, 2*(i+1));
}