/********************************************************************/
//strip, pdiffs, bdiffs, primers, barcodes, revPrimers
TrimOligos::TrimOligos(int p, int b, int l, int s, map<string, int> pr, map<string, int> br, vector<string> r, vector<string> lk, vector<string> sp){
/********************************************************************/
//strip, pdiffs, bdiffs, primers, barcodes, revPrimers
TrimOligos::TrimOligos(int p, int b, int l, int s, map<string, int> pr, map<string, int> br, vector<string> r, vector<string> lk, vector<string> sp){
- try {
-
- if (paired) { int success = stripPairedBarcode(seq, qual, group); return success; }
-
- string rawSequence = seq.getUnaligned();
- int success = bdiffs + 1; //guilty until proven innocent
-
- //can you find the barcode
- for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
- string oligo = it->first;
- if(rawSequence.length() < oligo.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(oligo, rawSequence.substr(0,oligo.length()))){
- group = it->second;
- seq.setUnaligned(rawSequence.substr(oligo.length()));
-
- if(qual.getName() != ""){
- qual.trimQScores(oligo.length(), -1);
- }
-
- 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 (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;
- int minCount = 1;
- int minGroup = -1;
- int minPos = 0;
-
- for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
- string oligo = it->first;
- // int length = oligo.length();
-
- if(rawSequence.length() < maxFBarcodeLength){ //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->alignPrimer(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--){
- if(oligo[i] != '-'){ alnLength = i+1; break; }
- }
- oligo = oligo.substr(0,alnLength);
- temp = temp.substr(0,alnLength);
+ try {
+
+ if (paired) { int success = stripPairedBarcode(seq, qual, group); return success; }
+
+ string rawSequence = seq.getUnaligned();
+ int success = bdiffs + 1; //guilty until proven innocent
+
+ //can you find the barcode
+ for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
+ string oligo = it->first;
+ if(rawSequence.length() < oligo.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(oligo, rawSequence.substr(0,oligo.length()))){
+ group = it->second;
+ seq.setUnaligned(rawSequence.substr(oligo.length()));
+
+ if(qual.getName() != ""){
+ qual.trimQScores(oligo.length(), -1);
+ }
+
+ 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 (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;
+ int minCount = 1;
+ int minGroup = -1;
+ int minPos = 0;
+
+ for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
+ string oligo = it->first;
+ // int length = oligo.length();
+
+ if(rawSequence.length() < maxFBarcodeLength){ //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->alignPrimer(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--){
+ if(oligo[i] != '-'){ alnLength = i+1; break; }
+ }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
-
- if(numDiff < minDiff){
- minDiff = numDiff;
- minCount = 1;
- minGroup = it->second;
- minPos = 0;
- for(int i=0;i<alnLength;i++){
- if(temp[i] != '-'){
- minPos++;
- }
- }
- }
- else if(numDiff == minDiff){
- minCount++;
- }
-
- }
-
- if(minDiff > bdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
- else{ //use the best match
- group = minGroup;
- seq.setUnaligned(rawSequence.substr(minPos));
-
- if(qual.getName() != ""){
- qual.trimQScores(minPos, -1);
- }
- success = minDiff;
- }
-
- if (alignment != NULL) { delete alignment; }
-
- }
-
- return success;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripBarcode");
- exit(1);
- }
+
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minGroup = it->second;
+ minPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ minPos++;
+ }
+ }
+ }
+ else if(numDiff == minDiff){
+ minCount++;
+ }
+
+ }
+
+ if(minDiff > bdiffs) { success = minDiff; } //no good matches
+ else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
+ else{ //use the best match
+ group = minGroup;
+ seq.setUnaligned(rawSequence.substr(minPos));
+
+ if(qual.getName() != ""){
+ qual.trimQScores(minPos, -1);
+ }
+ success = minDiff;
+ }
+
+ if (alignment != NULL) { delete alignment; }
+
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripBarcode");
+ exit(1);
+ }
- //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->alignPrimer(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);
+ //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->alignPrimer(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);
- //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->alignPrimer(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);
+ //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->alignPrimer(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);
- success = 0;
- break;
- }
- }
- //cout << "success=" << success << endl;
- //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;
+ success = 0;
+ break;
+ }
+ }
+ //cout << "success=" << success << endl;
+ //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;
- for(map<string, vector<int> >::iterator it=ifbarcodes.begin();it!=ifbarcodes.end();it++){
- string oligo = it->first;
-
- if(rawSeq.length() < maxFBarcodeLength){ //let's just assume that the barcodes are the same length
- success = bdiffs + 10;
- break;
- }
- //cout << "before = " << oligo << '\t' << rawSeq.substr(0,oligo.length()+bdiffs) << endl;
- //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->alignPrimer(oligo, rawSeq.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);
+ for(map<string, vector<int> >::iterator it=ifbarcodes.begin();it!=ifbarcodes.end();it++){
+ string oligo = it->first;
+
+ if(rawSeq.length() < maxFBarcodeLength){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10;
+ break;
+ }
+ //cout << "before = " << oligo << '\t' << rawSeq.substr(0,oligo.length()+bdiffs) << endl;
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawSeq.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);
- success = 0;
- break;
- }
- }
- //cout << "success=" << success << endl;
- //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;
+ success = 0;
+ break;
+ }
+ }
+ //cout << "success=" << success << endl;
+ //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;
- for(map<string, vector<int> >::iterator it=ifprimers.begin();it!=ifprimers.end();it++){
- string oligo = it->first;
-
- if(rawSeq.length() < maxFPrimerLength){ //let's just assume that the barcodes are the same length
- success = pdiffs + 10;
- break;
- }
- //cout << "before = " << oligo << '\t' << rawSeq.substr(0,oligo.length()+bdiffs) << endl;
- //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->alignPrimer(oligo, rawSeq.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);
+ for(map<string, vector<int> >::iterator it=ifprimers.begin();it!=ifprimers.end();it++){
+ string oligo = it->first;
+
+ if(rawSeq.length() < maxFPrimerLength){ //let's just assume that the barcodes are the same length
+ success = pdiffs + 10;
+ break;
+ }
+ //cout << "before = " << oligo << '\t' << rawSeq.substr(0,oligo.length()+bdiffs) << endl;
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawSeq.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);
- //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->alignPrimer(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);
+ //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->alignPrimer(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);
- //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->alignPrimer(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);
+ //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->alignPrimer(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);
- try {
-
- string rawSequence = seq.getUnaligned();
- int success = bdiffs + 1; //guilty until proven innocent
-
- //can you find the barcode
- for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
- string oligo = it->first;
- if(rawSequence.length() < oligo.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(oligo, rawSequence.substr(0,oligo.length()))){
- group = it->second;
- seq.setUnaligned(rawSequence.substr(oligo.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
+ try {
+
+ string rawSequence = seq.getUnaligned();
+ int success = bdiffs + 1; //guilty until proven innocent
+
+ //can you find the barcode
+ for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
+ string oligo = it->first;
+ if(rawSequence.length() < oligo.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(oligo, rawSequence.substr(0,oligo.length()))){
+ group = it->second;
+ seq.setUnaligned(rawSequence.substr(oligo.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
- 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;
- int minCount = 1;
- int minGroup = -1;
- int minPos = 0;
-
- for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
- string oligo = it->first;
- // int length = oligo.length();
-
- if(rawSequence.length() < maxFBarcodeLength){ //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->alignPrimer(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--){
- if(oligo[i] != '-'){ alnLength = i+1; break; }
- }
- oligo = oligo.substr(0,alnLength);
- temp = temp.substr(0,alnLength);
-
- int numDiff = countDiffs(oligo, temp);
-
- if(numDiff < minDiff){
- minDiff = numDiff;
- minCount = 1;
- minGroup = it->second;
- minPos = 0;
- for(int i=0;i<alnLength;i++){
- if(temp[i] != '-'){
- minPos++;
- }
- }
- }
- else if(numDiff == minDiff){
- minCount++;
- }
-
- }
-
- if(minDiff > bdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
- else{ //use the best match
- group = minGroup;
- seq.setUnaligned(rawSequence.substr(minPos));
- success = minDiff;
- }
-
- if (alignment != NULL) { delete alignment; }
-
- }
-
- return success;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripBarcode");
- exit(1);
- }
-
+ 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;
+ int minCount = 1;
+ int minGroup = -1;
+ int minPos = 0;
+
+ for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
+ string oligo = it->first;
+ // int length = oligo.length();
+
+ if(rawSequence.length() < maxFBarcodeLength){ //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->alignPrimer(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--){
+ if(oligo[i] != '-'){ alnLength = i+1; break; }
+ }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+
+ int numDiff = countDiffs(oligo, temp);
+
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minGroup = it->second;
+ minPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ minPos++;
+ }
+ }
+ }
+ else if(numDiff == minDiff){
+ minCount++;
+ }
+
+ }
+
+ if(minDiff > bdiffs) { success = minDiff; } //no good matches
+ else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
+ else{ //use the best match
+ group = minGroup;
+ seq.setUnaligned(rawSequence.substr(minPos));
+ success = minDiff;
+ }
+
+ if (alignment != NULL) { delete alignment; }
+
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripBarcode");
+ exit(1);
+ }
+
- try {
-
- string rawSequence = seq.getUnaligned();
- int success = pdiffs + 1; //guilty until proven innocent
-
- //can you find the primer
- for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
- string oligo = it->first;
- if(rawSequence.length() < oligo.length()){ //let's just assume that the primers are the same length
- success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
- break;
- }
-
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
- group = it->second;
- seq.setUnaligned(rawSequence.substr(oligo.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 (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;
- int minCount = 1;
- int minGroup = -1;
- int minPos = 0;
-
- for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
- string oligo = it->first;
- // int length = oligo.length();
-
- if(rawSequence.length() < maxFPrimerLength){
- success = pdiffs + 100;
- break;
- }
-
- //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->alignPrimer(oligo, rawSequence.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(numDiff < minDiff){
- minDiff = numDiff;
- minCount = 1;
- minGroup = it->second;
- minPos = 0;
- for(int i=0;i<alnLength;i++){
- if(temp[i] != '-'){
- minPos++;
- }
- }
- }
- else if(numDiff == minDiff){
- minCount++;
- }
-
- }
-
- if(minDiff > pdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = pdiffs + 10; } //can't tell the difference between multiple primers
- else{ //use the best match
- group = minGroup;
- seq.setUnaligned(rawSequence.substr(minPos));
- success = minDiff;
- }
-
- if (alignment != NULL) { delete alignment; }
-
- }
-
- return success;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripForward");
- exit(1);
- }
+ try {
+
+ string rawSequence = seq.getUnaligned();
+ int success = pdiffs + 1; //guilty until proven innocent
+
+ //can you find the primer
+ for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+ string oligo = it->first;
+ if(rawSequence.length() < oligo.length()){ //let's just assume that the primers are the same length
+ success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+
+ if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
+ group = it->second;
+ seq.setUnaligned(rawSequence.substr(oligo.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 (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;
+ int minCount = 1;
+ int minGroup = -1;
+ int minPos = 0;
+
+ for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+ string oligo = it->first;
+ // int length = oligo.length();
+
+ if(rawSequence.length() < maxFPrimerLength){
+ success = pdiffs + 100;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawSequence.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(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minGroup = it->second;
+ minPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ minPos++;
+ }
+ }
+ }
+ else if(numDiff == minDiff){
+ minCount++;
+ }
+
+ }
+
+ if(minDiff > pdiffs) { success = minDiff; } //no good matches
+ else if(minCount > 1) { success = pdiffs + 10; } //can't tell the difference between multiple primers
+ else{ //use the best match
+ group = minGroup;
+ seq.setUnaligned(rawSequence.substr(minPos));
+ success = minDiff;
+ }
+
+ if (alignment != NULL) { delete alignment; }
+
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripForward");
+ exit(1);
+ }
- try {
-
- if (paired) { int success = stripPairedPrimers(seq, qual, group, keepForward); return success; }
-
- string rawSequence = seq.getUnaligned();
- int success = pdiffs + 1; //guilty until proven innocent
-
- //can you find the primer
- for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
- string oligo = it->first;
- if(rawSequence.length() < oligo.length()){ //let's just assume that the primers are the same length
- success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
- break;
- }
-
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
- group = it->second;
- if (!keepForward) { seq.setUnaligned(rawSequence.substr(oligo.length())); }
- if(qual.getName() != ""){
- if (!keepForward) { qual.trimQScores(oligo.length(), -1); }
- }
- 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 (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;
- int minCount = 1;
- int minGroup = -1;
- int minPos = 0;
-
- for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
- string oligo = it->first;
- // int length = oligo.length();
-
- if(rawSequence.length() < maxFPrimerLength){
- success = pdiffs + 100;
- break;
- }
-
- //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->alignPrimer(oligo, rawSequence.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(numDiff < minDiff){
- minDiff = numDiff;
- minCount = 1;
- minGroup = it->second;
- minPos = 0;
- for(int i=0;i<alnLength;i++){
- if(temp[i] != '-'){
- minPos++;
- }
- }
- }
- else if(numDiff == minDiff){
- minCount++;
- }
-
- }
-
- if(minDiff > pdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = pdiffs + 10; } //can't tell the difference between multiple primers
- else{ //use the best match
- group = minGroup;
- if (!keepForward) { seq.setUnaligned(rawSequence.substr(minPos)); }
- if(qual.getName() != ""){
- if (!keepForward) { qual.trimQScores(minPos, -1); }
- }
- success = minDiff;
- }
-
- if (alignment != NULL) { delete alignment; }
-
- }
-
- return success;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripForward");
- exit(1);
- }
+ try {
+
+ if (paired) { int success = stripPairedPrimers(seq, qual, group, keepForward); return success; }
+
+ string rawSequence = seq.getUnaligned();
+ int success = pdiffs + 1; //guilty until proven innocent
+
+ //can you find the primer
+ for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+ string oligo = it->first;
+ if(rawSequence.length() < oligo.length()){ //let's just assume that the primers are the same length
+ success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
+ break;
+ }
+
+ if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
+ group = it->second;
+ if (!keepForward) { seq.setUnaligned(rawSequence.substr(oligo.length())); }
+ if(qual.getName() != ""){
+ if (!keepForward) { qual.trimQScores(oligo.length(), -1); }
+ }
+ 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 (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;
+ int minCount = 1;
+ int minGroup = -1;
+ int minPos = 0;
+
+ for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+ string oligo = it->first;
+ // int length = oligo.length();
+
+ if(rawSequence.length() < maxFPrimerLength){
+ success = pdiffs + 100;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawSequence.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(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minGroup = it->second;
+ minPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ minPos++;
+ }
+ }
+ }
+ else if(numDiff == minDiff){
+ minCount++;
+ }
+
+ }
+
+ if(minDiff > pdiffs) { success = minDiff; } //no good matches
+ else if(minCount > 1) { success = pdiffs + 10; } //can't tell the difference between multiple primers
+ else{ //use the best match
+ group = minGroup;
+ if (!keepForward) { seq.setUnaligned(rawSequence.substr(minPos)); }
+ if(qual.getName() != ""){
+ if (!keepForward) { qual.trimQScores(minPos, -1); }
+ }
+ success = minDiff;
+ }
+
+ if (alignment != NULL) { delete alignment; }
+
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripForward");
+ exit(1);
+ }
- try {
- string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
-
- for(int i=0;i<revPrimer.size();i++){
- string oligo = revPrimer[i];
-
- if(rawSequence.length() < oligo.length()){
- success = 0;
- break;
- }
-
- if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
- seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
- if(qual.getName() != ""){
- qual.trimQScores(-1, rawSequence.length()-oligo.length());
- }
- success = 1;
- break;
- }
- }
- return success;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripReverse");
- exit(1);
- }
+ try {
+ string rawSequence = seq.getUnaligned();
+ bool success = 0; //guilty until proven innocent
+
+ for(int i=0;i<revPrimer.size();i++){
+ string oligo = revPrimer[i];
+
+ if(rawSequence.length() < oligo.length()){
+ success = 0;
+ break;
+ }
+
+ if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
+ seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
+ if(qual.getName() != ""){
+ qual.trimQScores(-1, rawSequence.length()-oligo.length());
+ }
+ success = 1;
+ break;
+ }
+ }
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripReverse");
+ exit(1);
+ }
- try {
-
- string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
-
- for(int i=0;i<revPrimer.size();i++){
- string oligo = revPrimer[i];
-
- if(rawSequence.length() < oligo.length()){
- success = 0;
- break;
- }
-
- if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
- seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
- success = 1;
- break;
- }
- }
-
- return success;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripReverse");
- exit(1);
- }
+ try {
+
+ string rawSequence = seq.getUnaligned();
+ bool success = 0; //guilty until proven innocent
+
+ for(int i=0;i<revPrimer.size();i++){
+ string oligo = revPrimer[i];
+
+ if(rawSequence.length() < oligo.length()){
+ success = 0;
+ break;
+ }
+
+ if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
+ seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
+ success = 1;
+ break;
+ }
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripReverse");
+ exit(1);
+ }
- try {
- string rawSequence = seq.getUnaligned();
- bool success = ldiffs + 1; //guilty until proven innocent
-
- for(int i=0;i<linker.size();i++){
- string oligo = linker[i];
-
- if(rawSequence.length() < oligo.length()){
- success = ldiffs + 10;
- break;
- }
-
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
- seq.setUnaligned(rawSequence.substr(oligo.length()));
- if(qual.getName() != ""){
- qual.trimQScores(oligo.length(), -1);
- }
- success = 0;
- break;
- }
- }
+ try {
+ string rawSequence = seq.getUnaligned();
+ bool success = ldiffs + 1; //guilty until proven innocent
+
+ for(int i=0;i<linker.size();i++){
+ string oligo = linker[i];
+
+ if(rawSequence.length() < oligo.length()){
+ success = ldiffs + 10;
+ break;
+ }
+
+ if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
+ seq.setUnaligned(rawSequence.substr(oligo.length()));
+ if(qual.getName() != ""){
+ qual.trimQScores(oligo.length(), -1);
+ }
+ success = 0;
+ break;
+ }
+ }
- if ((ldiffs == 0) || (success == 0)) { return success; }
-
- else { //try aligning and see if you can find it
- Alignment* alignment;
- 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;
- int minCount = 1;
- int minPos = 0;
-
- for(int i = 0; i < linker.size(); i++){
- string oligo = linker[i];
- // int length = oligo.length();
-
- if(rawSequence.length() < maxLinkerLength){ //let's just assume that the barcodes are the same length
- success = ldiffs + 10;
- break;
- }
-
- //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+ldiffs));
- 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(numDiff < minDiff){
- minDiff = numDiff;
- minCount = 1;
- minPos = 0;
- for(int i=0;i<alnLength;i++){
- if(temp[i] != '-'){
- minPos++;
- }
- }
- }
- else if(numDiff == minDiff){
- minCount++;
- }
-
- }
-
- if(minDiff > ldiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = ldiffs + 100; } //can't tell the difference between multiple barcodes
- else{ //use the best match
- seq.setUnaligned(rawSequence.substr(minPos));
-
- if(qual.getName() != ""){
- qual.trimQScores(minPos, -1);
- }
- success = minDiff;
- }
-
- if (alignment != NULL) { delete alignment; }
-
- }
-
-
- return success;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripLinker");
- exit(1);
- }
+ if ((ldiffs == 0) || (success == 0)) { return success; }
+
+ else { //try aligning and see if you can find it
+ Alignment* alignment;
+ 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;
+ int minCount = 1;
+ int minPos = 0;
+
+ for(int i = 0; i < linker.size(); i++){
+ string oligo = linker[i];
+ // int length = oligo.length();
+
+ if(rawSequence.length() < maxLinkerLength){ //let's just assume that the barcodes are the same length
+ success = ldiffs + 10;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+ldiffs));
+ 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(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ minPos++;
+ }
+ }
+ }
+ else if(numDiff == minDiff){
+ minCount++;
+ }
+
+ }
+
+ if(minDiff > ldiffs) { success = minDiff; } //no good matches
+ else if(minCount > 1) { success = ldiffs + 100; } //can't tell the difference between multiple barcodes
+ else{ //use the best match
+ seq.setUnaligned(rawSequence.substr(minPos));
+
+ if(qual.getName() != ""){
+ qual.trimQScores(minPos, -1);
+ }
+ success = minDiff;
+ }
+
+ if (alignment != NULL) { delete alignment; }
+
+ }
+
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripLinker");
+ exit(1);
+ }
- if ((ldiffs == 0) || (success == 0)) { return success; }
-
- else { //try aligning and see if you can find it
- Alignment* alignment;
- 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;
- int minCount = 1;
- int minPos = 0;
-
- for(int i = 0; i < linker.size(); i++){
- string oligo = linker[i];
- // int length = oligo.length();
-
- if(rawSequence.length() < maxLinkerLength){ //let's just assume that the barcodes are the same length
- success = ldiffs + 10;
- break;
- }
-
- //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+ldiffs));
- 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(numDiff < minDiff){
- minDiff = numDiff;
- minCount = 1;
- minPos = 0;
- for(int i=0;i<alnLength;i++){
- if(temp[i] != '-'){
- minPos++;
- }
- }
- }
- else if(numDiff == minDiff){
- minCount++;
- }
-
- }
-
- if(minDiff > ldiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = ldiffs + 100; } //can't tell the difference between multiple barcodes
- else{ //use the best match
- seq.setUnaligned(rawSequence.substr(minPos));
- success = minDiff;
- }
-
- if (alignment != NULL) { delete alignment; }
-
- }
-
- return success;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripLinker");
- exit(1);
- }
+ if ((ldiffs == 0) || (success == 0)) { return success; }
+
+ else { //try aligning and see if you can find it
+ Alignment* alignment;
+ 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;
+ int minCount = 1;
+ int minPos = 0;
+
+ for(int i = 0; i < linker.size(); i++){
+ string oligo = linker[i];
+ // int length = oligo.length();
+
+ if(rawSequence.length() < maxLinkerLength){ //let's just assume that the barcodes are the same length
+ success = ldiffs + 10;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+ldiffs));
+ 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(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ minPos++;
+ }
+ }
+ }
+ else if(numDiff == minDiff){
+ minCount++;
+ }
+
+ }
+
+ if(minDiff > ldiffs) { success = minDiff; } //no good matches
+ else if(minCount > 1) { success = ldiffs + 100; } //can't tell the difference between multiple barcodes
+ else{ //use the best match
+ seq.setUnaligned(rawSequence.substr(minPos));
+ success = minDiff;
+ }
+
+ if (alignment != NULL) { delete alignment; }
+
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripLinker");
+ exit(1);
+ }
- try {
- string rawSequence = seq.getUnaligned();
- bool success = sdiffs+1; //guilty until proven innocent
-
- for(int i=0;i<spacer.size();i++){
- string oligo = spacer[i];
-
- if(rawSequence.length() < oligo.length()){
- success = sdiffs+10;
- break;
- }
-
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
- seq.setUnaligned(rawSequence.substr(oligo.length()));
- if(qual.getName() != ""){
- qual.trimQScores(oligo.length(), -1);
- }
- success = 0;
- break;
- }
- }
+ try {
+ string rawSequence = seq.getUnaligned();
+ bool success = sdiffs+1; //guilty until proven innocent
+
+ for(int i=0;i<spacer.size();i++){
+ string oligo = spacer[i];
+
+ if(rawSequence.length() < oligo.length()){
+ success = sdiffs+10;
+ break;
+ }
+
+ if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
+ seq.setUnaligned(rawSequence.substr(oligo.length()));
+ if(qual.getName() != ""){
+ qual.trimQScores(oligo.length(), -1);
+ }
+ success = 0;
+ break;
+ }
+ }
- if ((sdiffs == 0) || (success == 0)) { return success; }
-
- else { //try aligning and see if you can find it
- Alignment* alignment;
- 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;
- int minCount = 1;
- int minPos = 0;
-
- for(int i = 0; i < spacer.size(); i++){
- string oligo = spacer[i];
- // int length = oligo.length();
-
- if(rawSequence.length() < maxSpacerLength){ //let's just assume that the barcodes are the same length
- success = sdiffs + 10;
- break;
- }
-
- //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+sdiffs));
- 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(numDiff < minDiff){
- minDiff = numDiff;
- minCount = 1;
- minPos = 0;
- for(int i=0;i<alnLength;i++){
- if(temp[i] != '-'){
- minPos++;
- }
- }
- }
- else if(numDiff == minDiff){
- minCount++;
- }
-
- }
-
- if(minDiff > sdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = sdiffs + 100; } //can't tell the difference between multiple barcodes
- else{ //use the best match
- seq.setUnaligned(rawSequence.substr(minPos));
-
- if(qual.getName() != ""){
- qual.trimQScores(minPos, -1);
- }
- success = minDiff;
- }
-
- if (alignment != NULL) { delete alignment; }
-
- }
+ if ((sdiffs == 0) || (success == 0)) { return success; }
-
- return success;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripSpacer");
- exit(1);
- }
+ else { //try aligning and see if you can find it
+ Alignment* alignment;
+ 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;
+ int minCount = 1;
+ int minPos = 0;
+
+ for(int i = 0; i < spacer.size(); i++){
+ string oligo = spacer[i];
+ // int length = oligo.length();
+
+ if(rawSequence.length() < maxSpacerLength){ //let's just assume that the barcodes are the same length
+ success = sdiffs + 10;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+sdiffs));
+ 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(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ minPos++;
+ }
+ }
+ }
+ else if(numDiff == minDiff){
+ minCount++;
+ }
+
+ }
+
+ if(minDiff > sdiffs) { success = minDiff; } //no good matches
+ else if(minCount > 1) { success = sdiffs + 100; } //can't tell the difference between multiple barcodes
+ else{ //use the best match
+ seq.setUnaligned(rawSequence.substr(minPos));
+
+ if(qual.getName() != ""){
+ qual.trimQScores(minPos, -1);
+ }
+ success = minDiff;
+ }
+
+ if (alignment != NULL) { delete alignment; }
+
+ }
+
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripSpacer");
+ exit(1);
+ }
- if ((sdiffs == 0) || (success == 0)) { return success; }
-
- else { //try aligning and see if you can find it
- Alignment* alignment;
- 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;
- int minCount = 1;
- int minPos = 0;
-
- for(int i = 0; i < spacer.size(); i++){
- string oligo = spacer[i];
- // int length = oligo.length();
-
- if(rawSequence.length() < maxSpacerLength){ //let's just assume that the barcodes are the same length
- success = sdiffs + 10;
- break;
- }
-
- //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+sdiffs));
- 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(numDiff < minDiff){
- minDiff = numDiff;
- minCount = 1;
- minPos = 0;
- for(int i=0;i<alnLength;i++){
- if(temp[i] != '-'){
- minPos++;
- }
- }
- }
- else if(numDiff == minDiff){
- minCount++;
- }
-
- }
-
- if(minDiff > sdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = sdiffs + 100; } //can't tell the difference between multiple barcodes
- else{ //use the best match
- seq.setUnaligned(rawSequence.substr(minPos));
- success = minDiff;
- }
-
- if (alignment != NULL) { delete alignment; }
-
- }
-
- return success;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripSpacer");
- exit(1);
- }
+ if ((sdiffs == 0) || (success == 0)) { return success; }
+
+ else { //try aligning and see if you can find it
+ Alignment* alignment;
+ 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;
+ int minCount = 1;
+ int minPos = 0;
+
+ for(int i = 0; i < spacer.size(); i++){
+ string oligo = spacer[i];
+ // int length = oligo.length();
+
+ if(rawSequence.length() < maxSpacerLength){ //let's just assume that the barcodes are the same length
+ success = sdiffs + 10;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+sdiffs));
+ 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(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ minPos++;
+ }
+ }
+ }
+ else if(numDiff == minDiff){
+ minCount++;
+ }
+
+ }
+
+ if(minDiff > sdiffs) { success = minDiff; } //no good matches
+ else if(minCount > 1) { success = sdiffs + 100; } //can't tell the difference between multiple barcodes
+ else{ //use the best match
+ seq.setUnaligned(rawSequence.substr(minPos));
+ success = minDiff;
+ }
+
+ if (alignment != NULL) { delete alignment; }
+
+ }
+
+ return success;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "stripSpacer");
+ exit(1);
+ }
- try {
- bool success = 1;
- int length = oligo.length();
-
- for(int i=0;i<length;i++){
-
- if(oligo[i] != seq[i]){
- if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C') { success = 0; }
- else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { success = 0; }
- else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { success = 0; }
- else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { success = 0; }
- else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { success = 0; }
- else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { success = 0; }
- else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
-
- if(success == 0) { break; }
- }
- else{
- success = 1;
- }
- }
-
- return success;
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "compareDNASeq");
- exit(1);
- }
-
+ try {
+ bool success = 1;
+ int length = oligo.length();
+
+ for(int i=0;i<length;i++){
+
+ if(oligo[i] != seq[i]){
+ if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C') { success = 0; }
+ else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { success = 0; }
+ else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { success = 0; }
+ else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { success = 0; }
+ else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { success = 0; }
+ else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { success = 0; }
+ else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
+
+ if(success == 0) { break; }
+ }
+ else{
+ success = 1;
+ }
+ }
+
+ return success;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "compareDNASeq");
+ exit(1);
+ }
+
- try {
-
- int length = oligo.length();
- int countDiffs = 0;
-
- for(int i=0;i<length;i++){
-
- if(oligo[i] != seq[i]){
- if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.') { countDiffs++; }
- else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { countDiffs++; }
- else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { countDiffs++; }
- else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { countDiffs++; }
- else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { countDiffs++; }
- else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
- else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { countDiffs++; }
- else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
- else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
- else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
- else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { countDiffs++; }
- else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
- }
-
- }
-
- return countDiffs;
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "countDiffs");
- exit(1);
- }
+ try {
+
+ int length = oligo.length();
+ int countDiffs = 0;
+
+ for(int i=0;i<length;i++){
+
+ if(oligo[i] != seq[i]){
+ if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.') { countDiffs++; }
+ else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { countDiffs++; }
+ else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { countDiffs++; }
+ else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { countDiffs++; }
+ else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { countDiffs++; }
+ else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { countDiffs++; }
+ else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
+ }
+
+ }
+
+ return countDiffs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimOligos", "countDiffs");
+ exit(1);
+ }