try {
vector<data_struct> all; all.clear();
myQuery = *query;
-
+
for (int i = 0; i < refSeqs.size(); i++) {
for (int j = i+1; j < refSeqs.size(); j++) {
Sequence* q = new Sequence(query->getName(), query->getAligned());
Sequence* leftParent = new Sequence(refSeqs[i]->getName(), refSeqs[i]->getAligned());
Sequence* rightParent = new Sequence(refSeqs[j]->getName(), refSeqs[j]->getAligned());
+
+ //cout << q->getName() << endl << q->getAligned() << endl << endl;
+ //cout << leftParent->getName() << endl << leftParent->getAligned() << endl << endl;
+ //cout << rightParent->getName() << endl << rightParent->getAligned() << endl << endl;
+ //cout << " length = " << rightParent->getAligned().length() << endl;
map<int, int> spots; //map from spot in original sequence to spot in filtered sequence for query and both parents
vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
-
+// cout << "examining:\t" << refSeqs[i]->getName() << '\t' << refSeqs[j]->getName() << endl;
vector<data_struct> selectedDivs;
for (int k = 0; k < divs.size(); k++) {
int numSNPSLeft = snpsLeft.size();
int numSNPSRight = snpsRight.size();
+// cout << numSNPSLeft << '\t' << numSNPSRight << endl;
//require at least 4 SNPs on each side of the break
if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
//are we within 10 points of the bootstrap cutoff?
- if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
- bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
-
- if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
-
- divs[k].bsa = BS_A;
- divs[k].bsb = BS_B;
- divs[k].bsMax = max(BS_A, BS_B);
- divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
- }
+// if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
+// bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
+//
+// if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
+//
+// divs[k].bsa = BS_A;
+// divs[k].bsb = BS_B;
+// divs[k].bsMax = max(BS_A, BS_B);
+// divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
+// }
//so results reflect orignal alignment
divs[k].winLStart = spots[divs[k].winLStart];
int rightLength = length - leftLength;
float QLA = computePercentID(query, parentA, 0, breakpoint);
- float QRB = computePercentID(query, parentB, breakpoint+1, length);
+ float QRB = computePercentID(query, parentB, breakpoint+1, length-1);
float QLB = computePercentID(query, parentB, 0, breakpoint);
- float QRA = computePercentID(query, parentA, breakpoint+1, length);
+ float QRA = computePercentID(query, parentA, breakpoint+1, length-1);
float LAB = computePercentID(parentA, parentB, 0, breakpoint);
- float RAB = computePercentID(parentA, parentB, breakpoint+1, length);
-
+ float RAB = computePercentID(parentA, parentB, breakpoint+1, length-1);
+
float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length;
float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB));
float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB));
+
//cout << q->getName() << '\t';
//cout << pA->getName() << '\t';
//cout << pB->getName() << '\t';
- // cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB;
+ //cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB;
//cout << "\tCHIM_TYPE_B\t" << divR_QLB_QRA << "\tQLB: " << QLB << "\tQRA: " << QRA << "\tQLB_QRA: " << QLB_QRA << endl;
//cout << leftLength << '\t' << rightLength << '\t' << QLA << '\t' << QRB << '\t' << QLB << '\t' << QRA << '\t' << LAB << '\t' << RAB << '\t' << AB << '\t' << QA << '\t' << QB << '\t' << QLA_QRB << '\t' << QLB_QRA << endl;
}//if
}//for
+
return data;
}