void CHMM::FindFBDistance(CObsSeq *obsSeq, ostream &outFile, long snp_start, long snp_end)
{
double *scale;
double **alpha, **beta;
double logProb;
int i, j, em, t, k;
double **posterior;
double post;
for(i=1;i<=obsSeq->mNbSequences;i++){ // Loop over observation files:
long T = obsSeq->mNbObs[i];
CObs **obs = obsSeq->mObs[i];
alpha = SetMatrix(T, mN);// different size every time
beta = SetMatrix(T, mN);
scale = SetVector(T);
int *q = SetIntVector(T);
posterior = SetMatrix(T,mN);
// logProb contains log P(x)
// Haplotype Calling
logProb = ForwardAlgo(alpha, scale, obs, T, TRUE);
BackwardAlgo(beta, scale, obs, T);
for(t=1;t<=T;t++) {
READ *nd = (((CFlexibleObs<READ*>*)(obs[t]))->Get(1));
for(k=1;k<=mN;k++) {
// Experimental: P(x) cancels scaling for alpha and beta
// so posterior is just their product
double st = 1.0;
for(j=T; j>t; j--) {
st *= scale[j];
}
post = (alpha[t][k]*beta[t][k]*scale[t]);
#ifdef DEBUG
cout << endl;
cout << "Scale = " << scale[t] << endl;
cout << "Scaled alpha = " << alpha[t][k] << endl;
cout << "beta = " << beta[t][k] << endl;
cout << "Scaled beta = " << beta[t][k]*scale[t] << endl;
#endif
posterior[t][k] = post;
}
// REVISIT: hardcoding #states.
q[t] = posterior[t][1] > posterior[t][2] ? 1 : 2;
#ifdef DEBUG
//cout << "q[t] = " << q[t] << endl;
//cout << "posterior = " << posterior[t][q[t]] << endl;
#endif
nd->assignHaplotype(q[t],posterior[t][q[t]]);
}
UpdateGenotypes(snp_start, snp_end);
for(j=2;j<=T;j++) {
outFile << q[j] << "\t" << ((reads_list)[reads_list.size()-T+j-1])->GetPos() << endl;
}
delete [] q;
}
}
void NaiveBayes(int snp_start, int snp_end, int T)
{
int i, j, t;
SNP **known_snp_list = new SNP*[100];
int *known_index = new int[200];
int reads_list_size = reads_list.size();
for (t = 1+reads_list_size-T; t <= reads_list_size-1; t++) {
int known_snp_count = 0, flag = 0, direction = 1, hap = 0, mismatchsum = 0;
double norm = 0.0;
double emission_list[3], haprob[3], emission_set[3][100];
READ *pd = reads_list[t-1];
READ *nd = reads_list[t];
int plen = pd->GetLen();
int nlen = nd->GetLen();
int ppos = pd->GetPos();
int npos = nd->GetPos();
int rd_start = ppos < npos ? npos : ppos;
int rd_end = ppos+plen > npos+nlen ? npos+nlen-1 : ppos+plen-1;
//mismatchsum = GetMismatchSum(nd);
//if(mismatchsum>=50)
// continue;
GetKnownSnpList(known_snp_list, &known_snp_count, known_index, t);
// This adds the count of known overlapping snps between adjacent reads
(*nd).AddKnownCount(known_snp_count);
#ifdef DEBUG
if(known_snp_count>0)
cout << "Read " << nd->GetPos() << " ; "<< t << " and " << t+1 << ", " << rd_start << ", " << rd_end << " with " << known_snp_count << " known snps." << endl << endl;
cout << "SnpPos R A LL..\tAA_gen AA_obs AA_genob\tAB_gen AB_obs AB_genob\tBB_gen BB_obs BB_genob\tprob\n";
cout << "Throwing emissions from read: " << nd->GetPos() << endl;
#endif
for(j=1;j<=2;j++) {
#ifdef DEBUG
cout << "Haplotype " << j << endl;
#endif
emission_list[j] = 0.0;
for(int count=0; count<known_snp_count; count++) {
double emission;
SNP *sp = known_snp_list[count];
#ifdef DEBUG
cout << sp->GetPos() << " " << sp->GetRef() << " " << sp->GetAlt();
#endif
// Obtains naive bayes score for the count-th overlapping known snp
// between the adjacent reads for haplotype, 'j'.
// Working with relative haplotype here.
emission = compute_new_emission(known_snp_list, count, t, known_index, j);
if(emission==0.0)
continue;
emission_list[j] += ((emission));
emission_set[j][count] = emission;
}
#ifdef DEBUG
cout << "Total Emission = " << emission_list[j] << endl;
#endif
}
if(emission_set[1][0]<emission_set[2][0])
direction = 2;
for(int count=1; count<known_snp_count; count++) {
if(emission_set[1][count]>emission_set[2][count]&&direction==2)
flag = 1;
if(emission_set[1][count]<emission_set[2][count]&&direction==1)
flag = 1;
}
#ifdef DEBUG
cout << "Discordance = " << flag << endl;
#endif
norm = emission_list[1] + emission_list[2];
if(norm!=0.0) {
haprob[1] = emission_list[1] / norm;
haprob[2] = emission_list[2] / norm;
} else {
haprob[1] = 0.5;
haprob[2] = 0.5;
}
#ifdef DEBUG
cout << "Happrob[1] = " << haprob[1] << endl;
cout << "Happrob[2] = " << haprob[2] << endl;
#endif
// If haplotype probabilities are equal, randomly assign haplotype
hap = haprob[1] > haprob[2] ? 1 : haprob[1] == haprob[2] ? t%2+1 : 2;
double happrob = haprob[hap];
// convert relative haplotype to absolute haplotype
hap = (*pd).GetHap() == hap ? 1 : 2;
nd->assignHaplotype(hap, happrob, flag);
flag = 0; direction = 1;
}
delete [] known_index;
delete [] known_snp_list;
}