revPrimer = r;
linker = lk;
spacer = sp;
+ maxFBarcodeLength = 0;
+ for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
+ if(it->first.length() > maxFBarcodeLength){
+ maxFBarcodeLength = it->first.length();
+ }
+ }
+ maxFPrimerLength = 0;
+ map<string,int>::iterator it;
+ for(it=primers.begin();it!=primers.end();it++){
+ if(it->first.length() > maxFPrimerLength){
+ maxFPrimerLength = it->first.length();
+ }
+ }
+
+ maxLinkerLength = 0;
+ for(int i = 0; i < linker.size(); i++){
+ if(linker[i].length() > maxLinkerLength){
+ maxLinkerLength = linker[i].length();
+ }
+ }
+
+ maxSpacerLength = 0;
+ for(int i = 0; i < spacer.size(); i++){
+ if(spacer[i].length() > maxSpacerLength){
+ maxSpacerLength = spacer[i].length();
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "TrimOligos");
+ exit(1);
+ }
+}
+/********************************************************************/
+//strip, pdiffs, bdiffs, primers, barcodes, revPrimers
+TrimOligos::TrimOligos(int p, int b, int l, int s, map<int, oligosPair> pr, map<int, oligosPair> br){
+ try {
+ m = MothurOut::getInstance();
+
+ pdiffs = p;
+ bdiffs = b;
+ ldiffs = l;
+ sdiffs = s;
+
+ maxFBarcodeLength = 0;
+ for(map<int,oligosPair>::iterator it=br.begin();it!=br.end();it++){
+ string forward = it->second.forward;
+ map<string, vector<int> >::iterator itForward = ifbarcodes.find(forward);
+
+ if(forward.length() > maxFBarcodeLength){ maxFBarcodeLength = forward.length(); }
+
+ if (itForward == ifbarcodes.end()) {
+ vector<int> temp; temp.push_back(it->first);
+ ifbarcodes[forward] = temp;
+ }else { itForward->second.push_back(it->first); }
+ }
+
+ maxFPrimerLength = 0;
+ for(map<int,oligosPair>::iterator it=pr.begin();it!=pr.end();it++){
+ string forward = it->second.forward;
+ map<string, vector<int> >::iterator itForward = ifprimers.find(forward);
+
+ if(forward.length() > maxFPrimerLength){ maxFPrimerLength = forward.length(); }
+
+ if (itForward == ifprimers.end()) {
+ vector<int> temp; temp.push_back(it->first);
+ ifprimers[forward] = temp;
+ }else { itForward->second.push_back(it->first); }
+ }
+
+ maxRBarcodeLength = 0;
+ for(map<int,oligosPair>::iterator it=br.begin();it!=br.end();it++){
+ string forward = it->second.reverse;
+ map<string, vector<int> >::iterator itForward = irbarcodes.find(forward);
+
+ if(forward.length() > maxRBarcodeLength){ maxRBarcodeLength = forward.length(); }
+
+ if (itForward == irbarcodes.end()) {
+ vector<int> temp; temp.push_back(it->first);
+ irbarcodes[forward] = temp;
+ }else { itForward->second.push_back(it->first); }
+ }
+
+ maxRPrimerLength = 0;
+ for(map<int,oligosPair>::iterator it=pr.begin();it!=pr.end();it++){
+ string forward = it->second.reverse;
+ map<string, vector<int> >::iterator itForward = irprimers.find(forward);
+
+ if(forward.length() > maxRPrimerLength){ maxRPrimerLength = forward.length(); }
+
+ if (itForward == irprimers.end()) {
+ vector<int> temp; temp.push_back(it->first);
+ irprimers[forward] = temp;
+ }else { itForward->second.push_back(it->first); }
+ }
+
+ ipbarcodes = br;
+ ipprimers = pr;
}
catch(exception& e) {
m->errorOut(e, "TrimOligos", "TrimOligos");
if ((bdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (barcodes.size() > 0) {
- map<string,int>::iterator it;
-
- for(it=barcodes.begin();it!=barcodes.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
-
- }else{ alignment = NULL; }
+ if (barcodes.size() > 0) {alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxFBarcodeLength+bdiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = it->first;
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawSequence.length() < maxFBarcodeLength){ //let's just assume that the barcodes are the same length
success = bdiffs + 10;
break;
}
}
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
-
- int numDiff = countDiffs(oligo, temp);
+ int numDiff = countDiffs(oligo, temp);
if(numDiff < minDiff){
minDiff = numDiff;
m->errorOut(e, "TrimOligos", "stripBarcode");
exit(1);
}
+}
+//*******************************************************************/
+int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, int& group){
+ try {
+ //look for forward barcode
+ string rawFSequence = forwardSeq.getUnaligned();
+ string rawRSequence = reverseSeq.getUnaligned();
+ int success = bdiffs + 1; //guilty until proven innocent
+
+ //can you find the forward barcode
+ for(map<int,oligosPair>::iterator it=ipbarcodes.begin();it!=ipbarcodes.end();it++){
+ string foligo = it->second.forward;
+ string roligo = it->second.reverse;
+
+ if(rawFSequence.length() < foligo.length()){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+ if(rawRSequence.length() < roligo.length()){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+
+ if((compareDNASeq(foligo, rawFSequence.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawRSequence.substr((rawRSequence.length()-roligo.length()),roligo.length())))) {
+ group = it->first;
+ forwardSeq.setUnaligned(rawFSequence.substr(foligo.length()));
+ reverseSeq.setUnaligned(rawRSequence.substr(0,(rawRSequence.length()-roligo.length())));
+ success = 0;
+ break;
+ }
+ }
+
+ //if you found the barcode or if you don't want to allow for diffs
+ if ((bdiffs == 0) || (success == 0)) { return success; }
+ else { //try aligning and see if you can find it
+ Alignment* alignment;
+ if (ifbarcodes.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxFBarcodeLength+bdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ int minDiff = 1e6;
+ int minCount = 1;
+ vector< vector<int> > minFGroup;
+ vector<int> minFPos;
+
+ //the pair can have duplicates, but we only want to search for the unique forward and reverses, example
+ /*
+ 1 Sarah Westcott
+ 2 John Westcott
+ 3 Anna Westcott
+ 4 Sarah Schloss
+ 5 Pat Schloss
+ 6 Gail Brown
+ 7 Pat Moore
+
+ only want to look for forward = Sarah, John, Anna, Pat, Gail
+ reverse = Westcott, Schloss, Brown, Moore
+
+ but if best match forward = 4, and reverse = 1, we want to count as a valid match because forward 1 and forward 4 are the same. so both barcodes map to same group.
+ */
+ //cout << endl << forwardSeq.getName() << endl;
+ for(map<string, vector<int> >::iterator it=ifbarcodes.begin();it!=ifbarcodes.end();it++){
+ string oligo = it->first;
+
+ if(rawFSequence.length() < maxFBarcodeLength){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10;
+ break;
+ }
+ //cout << "before = " << oligo << '\t' << rawFSequence.substr(0,oligo.length()+bdiffs) << endl;
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->align(oligo, rawFSequence.substr(0,oligo.length()+bdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+
+ if (alnLength == 0) { numDiff = bdiffs + 100; }
+ //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minFGroup.clear();
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ minFPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }else if(numDiff == minDiff){
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }
+ }
+
+ //cout << minDiff << '\t' << minCount << '\t' << endl;
+ if(minDiff > bdiffs) { success = minDiff; } //no good matches
+ else{
+ //check for reverse match
+ if (alignment != NULL) { delete alignment; }
+
+ if (irbarcodes.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxRBarcodeLength+bdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ minDiff = 1e6;
+ minCount = 1;
+ vector< vector<int> > minRGroup;
+ vector<int> minRPos;
+
+ for(map<string, vector<int> >::iterator it=irbarcodes.begin();it!=irbarcodes.end();it++){
+ string oligo = it->first;
+ //cout << "before = " << oligo << '\t' << rawRSequence.substr(0,oligo.length()+bdiffs) << endl;
+ if(rawRSequence.length() < maxRBarcodeLength){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->align(oligo, rawRSequence.substr(0,oligo.length()+bdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+ if (alnLength == 0) { numDiff = bdiffs + 100; }
+
+ //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minRGroup.clear();
+ minRGroup.push_back(it->second);
+ int tempminRPos = 0;
+ minRPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ }else if(numDiff == minDiff){
+ int tempminRPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ minRGroup.push_back(it->second);
+ }
+
+ }
+
+ /*cout << minDiff << '\t' << minCount << '\t' << endl;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minFGroup[i].size(); j++) { cout << minFGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;
+ for (int i = 0; i < minRGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minRGroup[i].size(); j++) { cout << minRGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;*/
+ if(minDiff > bdiffs) { success = minDiff; } //no good matches
+ else {
+ bool foundMatch = false;
+ vector<int> matches;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ for (int j = 0; j < minFGroup[i].size(); j++) {
+ for (int k = 0; k < minRGroup.size(); k++) {
+ if (m->inUsersGroups(minFGroup[i][j], minRGroup[k])) { matches.push_back(minFGroup[i][j]); k+= minRGroup.size(); }
+ }
+ }
+ }
+
+ int fStart = 0;
+ int rStart = 0;
+ if (matches.size() == 1) {
+ foundMatch = true;
+ group = matches[0];
+ fStart = minFPos[0];
+ rStart = minRPos[0];
+ }
+
+ //we have an acceptable match for the forward and reverse, but do they match?
+ if (foundMatch) {
+ forwardSeq.setUnaligned(rawFSequence.substr(fStart));
+ reverseSeq.setUnaligned(rawRSequence.substr(rStart));
+ success = minDiff;
+ }else { success = bdiffs + 100; }
+ }
+ }
+
+ if (alignment != NULL) { delete alignment; }
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripIBarcode");
+ exit(1);
+ }
+
+}
+//*******************************************************************/
+int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, QualityScores& forwardQual, QualityScores& reverseQual, int& group){
+ try {
+ //look for forward barcode
+ string rawFSequence = forwardSeq.getUnaligned();
+ string rawRSequence = reverseSeq.getUnaligned();
+ int success = bdiffs + 1; //guilty until proven innocent
+
+ //can you find the forward barcode
+ for(map<int,oligosPair>::iterator it=ipbarcodes.begin();it!=ipbarcodes.end();it++){
+ string foligo = it->second.forward;
+ string roligo = it->second.reverse;
+
+ if(rawFSequence.length() < foligo.length()){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+ if(rawRSequence.length() < roligo.length()){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+
+ if((compareDNASeq(foligo, rawFSequence.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawRSequence.substr((rawRSequence.length()-roligo.length()),roligo.length())))) {
+ group = it->first;
+ forwardSeq.setUnaligned(rawFSequence.substr(foligo.length()));
+ reverseSeq.setUnaligned(rawRSequence.substr(0,(rawRSequence.length()-roligo.length())));
+ forwardQual.trimQScores(foligo.length(), -1);
+ reverseQual.trimQScores(-1, rawRSequence.length()-roligo.length());
+ success = 0;
+ break;
+ }
+ }
+
+ //if you found the barcode or if you don't want to allow for diffs
+ if ((bdiffs == 0) || (success == 0)) { return success; }
+ else { //try aligning and see if you can find it
+ Alignment* alignment;
+ if (ifbarcodes.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxFBarcodeLength+bdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ int minDiff = 1e6;
+ int minCount = 1;
+ vector< vector<int> > minFGroup;
+ vector<int> minFPos;
+
+ //the pair can have duplicates, but we only want to search for the unique forward and reverses, example
+ /*
+ 1 Sarah Westcott
+ 2 John Westcott
+ 3 Anna Westcott
+ 4 Sarah Schloss
+ 5 Pat Schloss
+ 6 Gail Brown
+ 7 Pat Moore
+
+ only want to look for forward = Sarah, John, Anna, Pat, Gail
+ reverse = Westcott, Schloss, Brown, Moore
+
+ but if best match forward = 4, and reverse = 1, we want to count as a valid match because forward 1 and forward 4 are the same. so both barcodes map to same group.
+ */
+ //cout << endl << forwardSeq.getName() << endl;
+ for(map<string, vector<int> >::iterator it=ifbarcodes.begin();it!=ifbarcodes.end();it++){
+ string oligo = it->first;
+
+ if(rawFSequence.length() < maxFBarcodeLength){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10;
+ break;
+ }
+ //cout << "before = " << oligo << '\t' << rawFSequence.substr(0,oligo.length()+bdiffs) << endl;
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->align(oligo, rawFSequence.substr(0,oligo.length()+bdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+
+ if (alnLength == 0) { numDiff = bdiffs + 100; }
+ //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minFGroup.clear();
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ minFPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }else if(numDiff == minDiff){
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }
+ }
+
+ //cout << minDiff << '\t' << minCount << '\t' << endl;
+ if(minDiff > bdiffs) { success = minDiff; } //no good matches
+ else{
+ //check for reverse match
+ if (alignment != NULL) { delete alignment; }
+
+ if (irbarcodes.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxRBarcodeLength+bdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ minDiff = 1e6;
+ minCount = 1;
+ vector< vector<int> > minRGroup;
+ vector<int> minRPos;
+
+ for(map<string, vector<int> >::iterator it=irbarcodes.begin();it!=irbarcodes.end();it++){
+ string oligo = it->first;
+ //cout << "before = " << oligo << '\t' << rawRSequence.substr(0,oligo.length()+bdiffs) << endl;
+ if(rawRSequence.length() < maxRBarcodeLength){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->align(oligo, rawRSequence.substr(0,oligo.length()+bdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+ if (alnLength == 0) { numDiff = bdiffs + 100; }
+
+ //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minRGroup.clear();
+ minRGroup.push_back(it->second);
+ int tempminRPos = 0;
+ minRPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ }else if(numDiff == minDiff){
+ int tempminRPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ minRGroup.push_back(it->second);
+ }
+
+ }
+
+ /*cout << minDiff << '\t' << minCount << '\t' << endl;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minFGroup[i].size(); j++) { cout << minFGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;
+ for (int i = 0; i < minRGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minRGroup[i].size(); j++) { cout << minRGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;*/
+ if(minDiff > bdiffs) { success = minDiff; } //no good matches
+ else {
+ bool foundMatch = false;
+ vector<int> matches;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ for (int j = 0; j < minFGroup[i].size(); j++) {
+ for (int k = 0; k < minRGroup.size(); k++) {
+ if (m->inUsersGroups(minFGroup[i][j], minRGroup[k])) { matches.push_back(minFGroup[i][j]); k+= minRGroup.size(); }
+ }
+ }
+ }
+
+ int fStart = 0;
+ int rStart = 0;
+ if (matches.size() == 1) {
+ foundMatch = true;
+ group = matches[0];
+ fStart = minFPos[0];
+ rStart = minRPos[0];
+ }
+
+ //we have an acceptable match for the forward and reverse, but do they match?
+ if (foundMatch) {
+ forwardSeq.setUnaligned(rawFSequence.substr(fStart));
+ reverseSeq.setUnaligned(rawRSequence.substr(rStart));
+ forwardQual.trimQScores(fStart, -1);
+ reverseQual.trimQScores(rStart, -1);
+ success = minDiff;
+ }else { success = bdiffs + 100; }
+ }
+ }
+
+ if (alignment != NULL) { delete alignment; }
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripIBarcode");
+ exit(1);
+ }
+
+}
+//*******************************************************************/
+int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, QualityScores& forwardQual, QualityScores& reverseQual, int& group){
+ try {
+ //look for forward barcode
+ string rawFSequence = forwardSeq.getUnaligned();
+ string rawRSequence = reverseSeq.getUnaligned();
+ int success = pdiffs + 1; //guilty until proven innocent
+
+ //can you find the forward barcode
+ for(map<int,oligosPair>::iterator it=ipprimers.begin();it!=ipprimers.end();it++){
+ string foligo = it->second.forward;
+ string roligo = it->second.reverse;
+
+ if(rawFSequence.length() < foligo.length()){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+ if(rawRSequence.length() < roligo.length()){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+
+ if((compareDNASeq(foligo, rawFSequence.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawRSequence.substr((rawRSequence.length()-roligo.length()),roligo.length())))) {
+ group = it->first;
+ forwardSeq.setUnaligned(rawFSequence.substr(foligo.length()));
+ reverseSeq.setUnaligned(rawRSequence.substr(0,(rawRSequence.length()-roligo.length())));
+ forwardQual.trimQScores(foligo.length(), -1);
+ reverseQual.trimQScores(-1, rawRSequence.length()-roligo.length());
+ success = 0;
+ break;
+ }
+ }
+
+ //if you found the barcode or if you don't want to allow for diffs
+ if ((pdiffs == 0) || (success == 0)) { return success; }
+ else { //try aligning and see if you can find it
+ Alignment* alignment;
+ if (ifprimers.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxFPrimerLength+pdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ int minDiff = 1e6;
+ int minCount = 1;
+ vector< vector<int> > minFGroup;
+ vector<int> minFPos;
+
+ //the pair can have duplicates, but we only want to search for the unique forward and reverses, example
+ /*
+ 1 Sarah Westcott
+ 2 John Westcott
+ 3 Anna Westcott
+ 4 Sarah Schloss
+ 5 Pat Schloss
+ 6 Gail Brown
+ 7 Pat Moore
+
+ only want to look for forward = Sarah, John, Anna, Pat, Gail
+ reverse = Westcott, Schloss, Brown, Moore
+
+ but if best match forward = 4, and reverse = 1, we want to count as a valid match because forward 1 and forward 4 are the same. so both barcodes map to same group.
+ */
+ //cout << endl << forwardSeq.getName() << endl;
+ for(map<string, vector<int> >::iterator it=ifprimers.begin();it!=ifprimers.end();it++){
+ string oligo = it->first;
+
+ if(rawFSequence.length() < maxFPrimerLength){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10;
+ break;
+ }
+ //cout << "before = " << oligo << '\t' << rawFSequence.substr(0,oligo.length()+pdiffs) << endl;
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->align(oligo, rawFSequence.substr(0,oligo.length()+pdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+
+ if (alnLength == 0) { numDiff = pdiffs + 100; }
+ //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minFGroup.clear();
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ minFPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }else if(numDiff == minDiff){
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }
+ }
+
+ //cout << minDiff << '\t' << minCount << '\t' << endl;
+ if(minDiff > pdiffs) { success = minDiff; } //no good matches
+ else{
+ //check for reverse match
+ if (alignment != NULL) { delete alignment; }
+
+ if (irbarcodes.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxRPrimerLength+pdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ minDiff = 1e6;
+ minCount = 1;
+ vector< vector<int> > minRGroup;
+ vector<int> minRPos;
+
+ for(map<string, vector<int> >::iterator it=irprimers.begin();it!=irprimers.end();it++){
+ string oligo = it->first;
+ //cout << "before = " << oligo << '\t' << rawRSequence.substr(0,oligo.length()+pdiffs) << endl;
+ if(rawRSequence.length() < maxRPrimerLength){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->align(oligo, rawRSequence.substr(0,oligo.length()+pdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+ if (alnLength == 0) { numDiff = pdiffs + 100; }
+
+ //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minRGroup.clear();
+ minRGroup.push_back(it->second);
+ int tempminRPos = 0;
+ minRPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ }else if(numDiff == minDiff){
+ int tempminRPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ minRGroup.push_back(it->second);
+ }
+
+ }
+
+ /*cout << minDiff << '\t' << minCount << '\t' << endl;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minFGroup[i].size(); j++) { cout << minFGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;
+ for (int i = 0; i < minRGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minRGroup[i].size(); j++) { cout << minRGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;*/
+ if(minDiff > pdiffs) { success = minDiff; } //no good matches
+ else {
+ bool foundMatch = false;
+ vector<int> matches;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ for (int j = 0; j < minFGroup[i].size(); j++) {
+ for (int k = 0; k < minRGroup.size(); k++) {
+ if (m->inUsersGroups(minFGroup[i][j], minRGroup[k])) { matches.push_back(minFGroup[i][j]); k+= minRGroup.size(); }
+ }
+ }
+ }
+
+ int fStart = 0;
+ int rStart = 0;
+ if (matches.size() == 1) {
+ foundMatch = true;
+ group = matches[0];
+ fStart = minFPos[0];
+ rStart = minRPos[0];
+ }
+
+ //we have an acceptable match for the forward and reverse, but do they match?
+ if (foundMatch) {
+ forwardSeq.setUnaligned(rawFSequence.substr(fStart));
+ reverseSeq.setUnaligned(rawRSequence.substr(rStart));
+ forwardQual.trimQScores(fStart, -1);
+ reverseQual.trimQScores(rStart, -1);
+ success = minDiff;
+ }else { success = pdiffs + 100; }
+ }
+ }
+
+ if (alignment != NULL) { delete alignment; }
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripIForward");
+ exit(1);
+ }
+
+}
+//*******************************************************************/
+int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, int& group){
+ try {
+ //look for forward barcode
+ string rawFSequence = forwardSeq.getUnaligned();
+ string rawRSequence = reverseSeq.getUnaligned();
+ int success = pdiffs + 1; //guilty until proven innocent
+
+ //can you find the forward barcode
+ for(map<int,oligosPair>::iterator it=ipprimers.begin();it!=ipprimers.end();it++){
+ string foligo = it->second.forward;
+ string roligo = it->second.reverse;
+
+ if(rawFSequence.length() < foligo.length()){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+ if(rawRSequence.length() < roligo.length()){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+
+ if((compareDNASeq(foligo, rawFSequence.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawRSequence.substr((rawRSequence.length()-roligo.length()),roligo.length())))) {
+ group = it->first;
+ forwardSeq.setUnaligned(rawFSequence.substr(foligo.length()));
+ reverseSeq.setUnaligned(rawRSequence.substr(0,(rawRSequence.length()-roligo.length())));
+ success = 0;
+ break;
+ }
+ }
+
+ //if you found the barcode or if you don't want to allow for diffs
+ if ((pdiffs == 0) || (success == 0)) { return success; }
+ else { //try aligning and see if you can find it
+ Alignment* alignment;
+ if (ifprimers.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxFPrimerLength+pdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ int minDiff = 1e6;
+ int minCount = 1;
+ vector< vector<int> > minFGroup;
+ vector<int> minFPos;
+
+ //the pair can have duplicates, but we only want to search for the unique forward and reverses, example
+ /*
+ 1 Sarah Westcott
+ 2 John Westcott
+ 3 Anna Westcott
+ 4 Sarah Schloss
+ 5 Pat Schloss
+ 6 Gail Brown
+ 7 Pat Moore
+
+ only want to look for forward = Sarah, John, Anna, Pat, Gail
+ reverse = Westcott, Schloss, Brown, Moore
+
+ but if best match forward = 4, and reverse = 1, we want to count as a valid match because forward 1 and forward 4 are the same. so both barcodes map to same group.
+ */
+ //cout << endl << forwardSeq.getName() << endl;
+ for(map<string, vector<int> >::iterator it=ifprimers.begin();it!=ifprimers.end();it++){
+ string oligo = it->first;
+
+ if(rawFSequence.length() < maxFPrimerLength){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10;
+ break;
+ }
+ //cout << "before = " << oligo << '\t' << rawFSequence.substr(0,oligo.length()+pdiffs) << endl;
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->align(oligo, rawFSequence.substr(0,oligo.length()+pdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+
+ if (alnLength == 0) { numDiff = pdiffs + 100; }
+ //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minFGroup.clear();
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ minFPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }else if(numDiff == minDiff){
+ minFGroup.push_back(it->second);
+ int tempminFPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminFPos++;
+ }
+ }
+ minFPos.push_back(tempminFPos);
+ }
+ }
+
+ //cout << minDiff << '\t' << minCount << '\t' << endl;
+ if(minDiff > pdiffs) { success = minDiff; } //no good matches
+ else{
+ //check for reverse match
+ if (alignment != NULL) { delete alignment; }
+
+ if (irbarcodes.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxRPrimerLength+pdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ minDiff = 1e6;
+ minCount = 1;
+ vector< vector<int> > minRGroup;
+ vector<int> minRPos;
+
+ for(map<string, vector<int> >::iterator it=irprimers.begin();it!=irprimers.end();it++){
+ string oligo = it->first;
+ //cout << "before = " << oligo << '\t' << rawRSequence.substr(0,oligo.length()+pdiffs) << endl;
+ if(rawRSequence.length() < maxRPrimerLength){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->align(oligo, rawRSequence.substr(0,oligo.length()+pdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+ if (alnLength == 0) { numDiff = pdiffs + 100; }
+
+ //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minRGroup.clear();
+ minRGroup.push_back(it->second);
+ int tempminRPos = 0;
+ minRPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ }else if(numDiff == minDiff){
+ int tempminRPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ minRGroup.push_back(it->second);
+ }
+
+ }
+
+ /*cout << minDiff << '\t' << minCount << '\t' << endl;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minFGroup[i].size(); j++) { cout << minFGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;
+ for (int i = 0; i < minRGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minRGroup[i].size(); j++) { cout << minRGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;*/
+ if(minDiff > pdiffs) { success = minDiff; } //no good matches
+ else {
+ bool foundMatch = false;
+ vector<int> matches;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ for (int j = 0; j < minFGroup[i].size(); j++) {
+ for (int k = 0; k < minRGroup.size(); k++) {
+ if (m->inUsersGroups(minFGroup[i][j], minRGroup[k])) { matches.push_back(minFGroup[i][j]); k+= minRGroup.size(); }
+ }
+ }
+ }
+
+ int fStart = 0;
+ int rStart = 0;
+ if (matches.size() == 1) {
+ foundMatch = true;
+ group = matches[0];
+ fStart = minFPos[0];
+ rStart = minRPos[0];
+ }
+
+ //we have an acceptable match for the forward and reverse, but do they match?
+ if (foundMatch) {
+ forwardSeq.setUnaligned(rawFSequence.substr(fStart));
+ reverseSeq.setUnaligned(rawRSequence.substr(rStart));
+ success = minDiff;
+ }else { success = pdiffs + 100; }
+ }
+ }
+
+ if (alignment != NULL) { delete alignment; }
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripIForward");
+ exit(1);
+ }
}
//*******************************************************************/
if ((bdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
- Alignment* alignment;
- if (barcodes.size() > 0) {
- map<string,int>::iterator it=barcodes.begin();
-
- for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
-
- }else{ alignment = NULL; }
+ Alignment* alignment;
+ if (barcodes.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxFBarcodeLength+bdiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = it->first;
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawSequence.length() < maxFBarcodeLength){ //let's just assume that the barcodes are the same length
success = bdiffs + 10;
break;
}
alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
-
+
int alnLength = oligo.length();
for(int i=oligo.length()-1;i>=0;i--){
}
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
-
+
int numDiff = countDiffs(oligo, temp);
if(numDiff < minDiff){
}
}
-//********************************************************************/
+
+/********************************************************************/
int TrimOligos::stripForward(Sequence& seq, int& group){
try {
if ((pdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (primers.size() > 0) {
- map<string,int>::iterator it;
-
- for(it=primers.begin();it!=primers.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
-
- }else{ alignment = NULL; }
+ if (primers.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxFPrimerLength+pdiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = it->first;
// int length = oligo.length();
- if(rawSequence.length() < maxLength){
+ if(rawSequence.length() < maxFPrimerLength){
success = pdiffs + 100;
break;
}
if ((pdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (primers.size() > 0) {
- map<string,int>::iterator it;
-
- for(it=primers.begin();it!=primers.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
-
- }else{ alignment = NULL; }
+ if (primers.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxFPrimerLength+pdiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = it->first;
// int length = oligo.length();
- if(rawSequence.length() < maxLength){
+ if(rawSequence.length() < maxFPrimerLength){
success = pdiffs + 100;
break;
}
if ((ldiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (linker.size() > 0) {
- for(int i = 0; i < linker.size(); i++){
- if(linker[i].length() > maxLength){
- maxLength = linker[i].length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+ldiffs+1));
-
- }else{ alignment = NULL; }
+ if (linker.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLinkerLength+ldiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = linker[i];
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawSequence.length() < maxLinkerLength){ //let's just assume that the barcodes are the same length
success = ldiffs + 10;
break;
}
if ((ldiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (linker.size() > 0) {
- for(int i = 0; i < linker.size(); i++){
- if(linker[i].length() > maxLength){
- maxLength = linker[i].length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+ldiffs+1));
-
- }else{ alignment = NULL; }
+ if (linker.size() > 0) {alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLinkerLength+ldiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = linker[i];
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawSequence.length() < maxLinkerLength){ //let's just assume that the barcodes are the same length
success = ldiffs + 10;
break;
}
if ((sdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (spacer.size() > 0) {
- for(int i = 0; i < spacer.size(); i++){
- if(spacer[i].length() > maxLength){
- maxLength = spacer[i].length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+sdiffs+1));
-
- }else{ alignment = NULL; }
+ if (spacer.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxSpacerLength+sdiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = spacer[i];
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawSequence.length() < maxSpacerLength){ //let's just assume that the barcodes are the same length
success = sdiffs + 10;
break;
}
if ((sdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-
- int maxLength = 0;
-
Alignment* alignment;
- if (spacer.size() > 0) {
- for(int i = 0; i < spacer.size(); i++){
- if(spacer[i].length() > maxLength){
- maxLength = spacer[i].length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+sdiffs+1));
-
- }else{ alignment = NULL; }
+ if (spacer.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxSpacerLength+sdiffs+1)); }
+ else{ alignment = NULL; }
//can you find the barcode
int minDiff = 1e6;
string oligo = spacer[i];
// int length = oligo.length();
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
+ if(rawSequence.length() < maxSpacerLength){ //let's just assume that the barcodes are the same length
success = sdiffs + 10;
break;
}
projects / mothur.git / blobdiff