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];
selectedDivs.push_back(divs[k]);
}
}
-
+
//save selected
for (int mi = 0; mi < selectedDivs.size(); mi++) { all.push_back(selectedDivs[mi]); }
}
}
+
// compute bootstrap support
if (all.size() > 0) {
//sort them
int breakpoint = i;
int leftLength = breakpoint + 1;
int rightLength = length - leftLength;
-
+
float QLA = computePercentID(query, parentA, 0, breakpoint);
- float QRB = computePercentID(query, parentB, breakpoint+1, length - 1);
+ float QRB = computePercentID(query, parentB, breakpoint+1, length-1);
float QLB = computePercentID(query, parentB, 0, breakpoint);
- float QRA = computePercentID(query, parentA, breakpoint+1, length - 1);
+ float QRA = computePercentID(query, parentA, breakpoint+1, length-1);
float LAB = computePercentID(parentA, parentB, 0, breakpoint);
- float RAB = computePercentID(parentA, parentB, breakpoint+1, length - 1);
-
+ 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;
member.winLEnd = breakpoint;
member.winRStart = breakpoint+1;
member.winREnd = length-1;
- member.querySeq = *(q);
+ member.querySeq = *(q);
member.parentA = *(pA);
member.parentB = *(pB);
member.bsa = 0;
}//if
}//for
+
return data;
}
try {
vector<snps> data;
-//cout << left << '\t' << right << endl;
+
for (int i = left; i <= right; i++) {
char A = parentA[i];
char B = parentB[i];
if ((A != Q) || (B != Q)) {
-//cout << "not equal " << Q << '\t' << A << '\t' << B << endl;
-
+
//ensure not neighboring a gap. change to 12/09 release of chimeraSlayer - not sure what this adds, but it eliminates alot of SNPS
+
+
if (
//did query loose a base here during filter??
( i == 0 || abs (baseSpots[0][i] - baseSpots[0][i-1]) == 1) &&
- ( i == query.length() || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1)
+ ( i == query.length()-1 || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1)
&&
//did parentA loose a base here during filter??
( i == 0 || abs (baseSpots[1][i] - baseSpots[1][i-1]) == 1) &&
- ( i == parentA.length() || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1)
+ ( i == parentA.length()-1 || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1)
&&
//did parentB loose a base here during filter??
( i == 0 || abs (baseSpots[2][i] - baseSpots[2][i-1]) == 1) &&
- ( i == parentB.length() || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1)
+ ( i == parentB.length()-1 || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1)
)
{
-
snps member;
member.queryChar = Q;
member.parentAChar = A;
member.parentBChar = B;
-//cout << "not neighboring a gap " << Q << '\t' << A << '\t' << B << '\t' << baseSpots[0][i] << '\t' << baseSpots[0][i+1] << '\t' << baseSpots[0][i-1] << '\t' << baseSpots[1][i] << '\t' << baseSpots[1][i+1] << '\t' << baseSpots[1][i-1] << '\t' << baseSpots[2][i] << '\t' << baseSpots[2][i+1] << '\t' << baseSpots[2][i-1] << endl;
data.push_back(member);
}
}
-// cout << i << '\t' << data.size() << endl;
}
return data;
int numLeft = max(1, int(left.size() * percentSNPSample/(float)100 + 0.5));
int numRight = max(1, int(right.size() * percentSNPSample/(float)100 + 0.5));
- //cout << numLeft << '\t' << numRight << endl;
+
for (int i = 0; i < numIters; i++) {
//random sampling with replacement.
}
}
}
+
}
float numBases = (countA + countB) /(float) 2;
if (numBases == 0) { return 0; }
float percentIdentical = (numIdentical/(float)numBases) * 100;
-
+
return percentIdentical;
}
projects / mothur.git / blobdiff