// function added 10/24/2014
void update_neighbor_scores(struct SNPfrags* snpfrag,int node,int startnode,int secondnode,struct fragment* Flist,char* hap,struct PHEAP* pheap,int* slist)
{
// for all vertices linked to node -> update score of the neighbors, can be done using list of fragments for snpfrag[node]
int j=0,f=0,i=0,n=0,k=0,newnode=0;
char allele,allele1; float q2,q1,p1,p2,ew,match;
double oldscore=0;
for (n=0;n<snpfrag[node].frags;n++)
{
f = snpfrag[node].flist[n]; // index into Flist global
for (j=0;j<Flist[f].blocks;j++) // first find the allele at 'node' in the fragment 'f'
{
for (k=0;k<Flist[f].list[j].len;k++)
{
if (Flist[f].list[j].offset + k == node) { allele = Flist[f].list[j].hap[k]; q1 = Flist[f].list[j].pv[k]; }
}
}
for (j=0;j<Flist[f].blocks;j++)
{
for (k=0;k<Flist[f].list[j].len;k++)
{
allele1 = Flist[f].list[j].hap[k]; q2 = Flist[f].list[j].pv[k]; newnode = Flist[f].list[j].offset + k;
if (newnode == node || newnode == startnode || newnode == secondnode) continue;
p1 = q1*q2+(1-q1)*(1-q2); p2 = q1*(1-q2)+q2*(1-q1); ew = log10(p1/p2);
if (hap[node] == hap[Flist[f].list[j].offset + k] && allele == allele1) match = 1;
else if (hap[node] != hap[Flist[f].list[j].offset + k] && allele != allele1) match = 1;
else if (hap[node] == hap[Flist[f].list[j].offset + k] && allele != allele1) match = -1;
else if (hap[node] != hap[Flist[f].list[j].offset + k] && allele == allele1) match = -1;
if (snpfrag[node].parent == startnode)
{
oldscore = snpfrag[newnode].score; snpfrag[newnode].score += match*ew;
}
else if (snpfrag[node].parent == secondnode)
{
oldscore = snpfrag[newnode].score; snpfrag[newnode].score -= match*ew;
}
if (fabsf(oldscore) > fabsf(snpfrag[newnode].score)) // score decreased
{
pmaxHeapify(pheap,snpfrag[newnode].heaploc,snpfrag,slist);
}
else pbubbleUp(pheap,snpfrag[newnode].heaploc,snpfrag,slist);
}
}
}
}
void update_fragment_scores(struct SNPfrags* snpfrag, struct fragment* Flist, char* hap, int startnode, int secondnode, int node_added, struct PHEAP* pheap, int* slist) {
int j = 0, f = 0, t = 0, n = 0, k = 0, node = 0;
float prob, prob2;
float scores[4];
float Lo, Ln;
float Lo_htrans, Ln_htrans;
float f_scores[4];
float htrans_f_scores[4];
float oldscore;
int htrans_flipped = 0;
for (n = 0; n < snpfrag[node_added].frags; n++){
f = snpfrag[node_added].flist[n]; // index into Flist global
for (t = 0; t < 4; t++) f_scores[t] = Flist[f].scores[t]; // store previous fragment scores before updating
for (t = 0; t < 4; t++) htrans_f_scores[t] = Flist[f].htscores[t]; // store previous fragment scores before updating
j = snpfrag[node_added].jlist[n];
k = snpfrag[node_added].klist[n];
if (hap[Flist[f].list[j].offset + k] == '-' || (int) Flist[f].list[j].qv[k] - QVoffset < MINQ) continue;
node = Flist[f].list[j].offset + k;
if (node != node_added) continue;
prob = QVoffset - (int) Flist[f].list[j].qv[k];
prob /= 10; // log10(e)
prob2 = Flist[f].list[j].p1[k];
if (snpfrag[node].parent == startnode){ // if node is added to 'startnode', original and new likelihoods are updated identically
if (hap[node] == Flist[f].list[j].hap[k]){
Flist[f].scores[0] += prob2;
Flist[f].scores[1] += prob;
Flist[f].scores[2] += prob2;
Flist[f].scores[3] += prob;
} else {
Flist[f].scores[0] += prob;
Flist[f].scores[1] += prob2;
Flist[f].scores[2] += prob;
Flist[f].scores[3] += prob2;
}
} else if (snpfrag[node].parent == secondnode){
if (hap[node] == Flist[f].list[j].hap[k]){
Flist[f].scores[0] += prob;
Flist[f].scores[1] += prob2;
Flist[f].scores[2] += prob;
Flist[f].scores[3] += prob2;
} else {
Flist[f].scores[0] += prob2;
Flist[f].scores[1] += prob;
Flist[f].scores[2] += prob2;
Flist[f].scores[3] += prob;
}
}
if (HIC && Flist[f].data_type == 1){ // HiC read
htrans_flipped = (Flist[f].mate2_ix != -1 && node >= Flist[f].mate2_ix); // are we flipped due to h-trans?
if ((snpfrag[node].parent == startnode && !htrans_flipped)
||(snpfrag[node].parent == secondnode && htrans_flipped)){ // if node is added to 'startnode', original and new likelihoods are updated identically
if (hap[node] == Flist[f].list[j].hap[k]){
Flist[f].htscores[0] += prob2;
Flist[f].htscores[1] += prob;
Flist[f].htscores[2] += prob2;
Flist[f].htscores[3] += prob;
} else {
Flist[f].htscores[0] += prob;
Flist[f].htscores[1] += prob2;
Flist[f].htscores[2] += prob;
Flist[f].htscores[3] += prob2;
}
}else if((snpfrag[node].parent == secondnode && !htrans_flipped)
||(snpfrag[node].parent == startnode && htrans_flipped)){
if (hap[node] == Flist[f].list[j].hap[k]){
Flist[f].htscores[0] += prob;
Flist[f].htscores[1] += prob2;
Flist[f].htscores[2] += prob;
Flist[f].htscores[3] += prob2;
} else {
Flist[f].htscores[0] += prob2;
Flist[f].htscores[1] += prob;
Flist[f].htscores[2] += prob2;
Flist[f].htscores[3] += prob;
}
}
}
for (j = 0; j < Flist[f].blocks; j++){ // update score of every node outside 2 shores covered by 'f'
for (k = 0; k < Flist[f].list[j].len; k++) {
if (hap[Flist[f].list[j].offset + k] == '-' || (int) Flist[f].list[j].qv[k] - QVoffset < MINQ) continue;
node = Flist[f].list[j].offset + k;
if (snpfrag[node].parent != startnode && snpfrag[node].parent != secondnode && node != node_added) {
oldscore = snpfrag[node].score; // store old score
prob = QVoffset - (int) Flist[f].list[j].qv[k];
prob /= 10; // log10(e)
//prob1 = 1.0 - pow(10,prob); prob2 = log10(prob1);
prob2 = Flist[f].list[j].p1[k];
for (t = 0; t < 4; t++) scores[t] = f_scores[t];
if (hap[node] == Flist[f].list[j].hap[k]) {
scores[0] += prob2;
scores[1] += prob;
scores[2] += prob;
scores[3] += prob2;
} else {
scores[0] += prob;
scores[1] += prob2;
scores[2] += prob2;
scores[3] += prob;
}
Lo = addlogs(scores[0], scores[1]);
Ln = addlogs(scores[2], scores[3]);
if (HIC && Flist[f].data_type == 1){ // HiC Read
htrans_flipped = (Flist[f].mate2_ix != -1 && node >= Flist[f].mate2_ix); // are we flipped due to h-trans?
for (t = 0; t < 4; t++) scores[t] = htrans_f_scores[t];
if ((hap[node] == Flist[f].list[j].hap[k] && !htrans_flipped)
||(hap[node] != Flist[f].list[j].hap[k] && htrans_flipped)) {
scores[0] += prob2;
scores[1] += prob;
scores[2] += prob;
scores[3] += prob2;
} else {
scores[0] += prob;
scores[1] += prob2;
scores[2] += prob2;
scores[3] += prob;
}
Lo_htrans = addlogs(scores[0], scores[1]);
Ln_htrans = addlogs(scores[2], scores[3]);
// update Lo and Ln for h-trans possibility
Lo = addlogs(Lo+subtractlogs(0,Flist[f].htrans_prob), Lo_htrans+Flist[f].htrans_prob);
Ln = addlogs(Ln+subtractlogs(0,Flist[f].htrans_prob), Ln_htrans+Flist[f].htrans_prob);
}
snpfrag[node].score -= Lo - Ln;; // subtract old score for variant
for (t = 0; t < 4; t++) scores[t] = Flist[f].scores[t];
if (hap[node] == Flist[f].list[j].hap[k]) {
scores[0] += prob2;
scores[1] += prob;
scores[2] += prob;
scores[3] += prob2;
} else {
scores[0] += prob;
scores[1] += prob2;
scores[2] += prob2;
scores[3] += prob;
}
Lo = addlogs(scores[0], scores[1]);
Ln = addlogs(scores[2], scores[3]);
if (HIC && Flist[f].data_type == 1){ // HiC read
for (t = 0; t < 4; t++) scores[t] = Flist[f].htscores[t];
if ((hap[node] == Flist[f].list[j].hap[k] && !htrans_flipped)
||(hap[node] != Flist[f].list[j].hap[k] && htrans_flipped)) {
scores[0] += prob2;
scores[1] += prob;
scores[2] += prob;
scores[3] += prob2;
} else {
scores[0] += prob;
scores[1] += prob2;
scores[2] += prob2;
scores[3] += prob;
}
Lo_htrans = addlogs(scores[0], scores[1]);
Ln_htrans = addlogs(scores[2], scores[3]);
// update Lo and Ln for h-trans possibility
Lo = addlogs(Lo+subtractlogs(0,Flist[f].htrans_prob), Lo_htrans+Flist[f].htrans_prob);
Ln = addlogs(Ln+subtractlogs(0,Flist[f].htrans_prob), Ln_htrans+Flist[f].htrans_prob);
}
snpfrag[node].score += Lo - Ln; // add new delta LL for variant
if (fabsf(oldscore) > fabsf(snpfrag[node].score)){ // score decreased
pmaxHeapify(pheap, snpfrag[node].heaploc, snpfrag, slist);
} else pbubbleUp(pheap, snpfrag[node].heaploc, snpfrag, slist);
}
}
}
}
}