X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimoligos.cpp;h=e0f093c011e5c3ce97f62a22421e4145bded0325;hb=5ca84bbe4393adecc30dc05d64e79091ef35c40f;hp=a53f4e85388f0f7bbb6fda40c2074b4f555e29d3;hpb=7f1aca4ed9e6db70de82e80ca4771f7680b21d26;p=mothur.git diff --git a/trimoligos.cpp b/trimoligos.cpp index a53f4e8..e0f093c 100644 --- a/trimoligos.cpp +++ b/trimoligos.cpp @@ -17,6 +17,7 @@ TrimOligos::TrimOligos(int p, int b, int l, int s, map pr, map br, vector r, vector lk, vector sp){ try { m = MothurOut::getInstance(); + paired = false; pdiffs = p; bdiffs = b; @@ -71,6 +72,7 @@ TrimOligos::TrimOligos(int p, int b, int l, int s, map pr, map< bdiffs = b; ldiffs = l; sdiffs = s; + paired = true; maxFBarcodeLength = 0; for(map::iterator it=br.begin();it!=br.end();it++){ @@ -144,6 +146,7 @@ TrimOligos::TrimOligos(int p, int b, map pr, map br, v barcodes = br; primers = pr; revPrimer = r; + paired = false; maxFBarcodeLength = 0; for(map::iterator it=barcodes.begin();it!=barcodes.end();it++){ @@ -224,7 +227,7 @@ bool TrimOligos::findForward(Sequence& seq, int& primerStart, int& primerEnd){ string rawChunk = rawSequence.substr(j, olength+pdiffs); //use needleman to align first primer.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawChunk); + alignment->alignPrimer(oligo, rawChunk); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -302,6 +305,8 @@ bool TrimOligos::findReverse(Sequence& seq, int& primerStart, int& primerEnd){ int TrimOligos::stripBarcode(Sequence& seq, QualityScores& qual, int& group){ try { + if (paired) { int success = stripPairedBarcode(seq, qual, group); return success; } + string rawSequence = seq.getUnaligned(); int success = bdiffs + 1; //guilty until proven innocent @@ -350,7 +355,7 @@ int TrimOligos::stripBarcode(Sequence& seq, QualityScores& qual, int& group){ } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs)); + alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+bdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -473,7 +478,7 @@ int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, int& gr } //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)); + alignment->alignPrimer(oligo, rawFSequence.substr(0,oligo.length()+bdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -536,7 +541,7 @@ int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, int& gr } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawRSequence.substr(0,oligo.length()+bdiffs)); + alignment->alignPrimer(oligo, rawRSequence.substr(0,oligo.length()+bdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -700,7 +705,7 @@ int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, Quality } //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)); + alignment->alignPrimer(oligo, rawFSequence.substr(0,oligo.length()+bdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -763,7 +768,7 @@ int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, Quality } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawRSequence.substr(0,oligo.length()+bdiffs)); + alignment->alignPrimer(oligo, rawRSequence.substr(0,oligo.length()+bdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -858,6 +863,484 @@ int TrimOligos::stripBarcode(Sequence& forwardSeq, Sequence& reverseSeq, Quality } } +//*******************************************************************/ +int TrimOligos::stripPairedBarcode(Sequence& seq, QualityScores& qual, int& group){ + try { + //look for forward barcode + string rawSeq = seq.getUnaligned(); + int success = bdiffs + 1; //guilty until proven innocent + //cout << seq.getName() << endl; + //can you find the forward barcode + for(map::iterator it=ipbarcodes.begin();it!=ipbarcodes.end();it++){ + string foligo = it->second.forward; + string roligo = it->second.reverse; + //cout << it->first << '\t' << foligo << '\t' << roligo << endl; + //cout << it->first << '\t' << rawSeq.substr(0,foligo.length()) << '\t' << rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length()) << endl; + if(rawSeq.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(rawSeq.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, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) { + group = it->first; + string trimmedSeq = rawSeq.substr(foligo.length()); //trim forward barcode + seq.setUnaligned(trimmedSeq.substr(0,(trimmedSeq.length()-roligo.length()))); //trim reverse barcode + if(qual.getName() != ""){ + qual.trimQScores(-1, rawSeq.length()-roligo.length()); + qual.trimQScores(foligo.length(), -1); + } + 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 > minFGroup; + vector 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 >::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); + 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;isecond); + int tempminFPos = 0; + for(int i=0;i 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 > minRGroup; + vector minRPos; + + string rawRSequence = reverseOligo(seq.getUnaligned()); + //cout << irbarcodes.size() << '\t' << maxRBarcodeLength << endl; + for(map >::iterator it=irbarcodes.begin();it!=irbarcodes.end();it++){ + string oligo = reverseOligo(it->first); + //cout << "r before = " << reverseOligo(oligo) << '\t' << reverseOligo(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->alignPrimer(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 << "r after = " << reverseOligo(oligo) << '\t' << reverseOligo(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;isecond); + } + + } + + /*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 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 = rawSeq.length() - minRPos[0]; + } + + //we have an acceptable match for the forward and reverse, but do they match? + if (foundMatch) { + string trimmedSeq = rawSeq.substr(0, rStart); //trim reverse barcode + seq.setUnaligned(trimmedSeq.substr(fStart)); //trim forward barcode + if(qual.getName() != ""){ + qual.trimQScores(-1, rStart); + qual.trimQScores(fStart, -1); + } + success = minDiff; + //cout << "barcode = " << ipbarcodes[group].forward << '\t' << ipbarcodes[group].reverse << endl; + }else { success = bdiffs + 100; } + } + } + + if (alignment != NULL) { delete alignment; } + } + + return success; + + } + catch(exception& e) { + m->errorOut(e, "TrimOligos", "stripPairedBarcode"); + exit(1); + } + +} +//*******************************************************************/ +int TrimOligos::stripPairedPrimers(Sequence& seq, QualityScores& qual, int& group, bool keepForward){ + try { + //look for forward + string rawSeq = seq.getUnaligned(); + int success = pdiffs + 1; //guilty until proven innocent + //cout << seq.getName() << endl; + //can you find the forward + for(map::iterator it=ipprimers.begin();it!=ipprimers.end();it++){ + string foligo = it->second.forward; + string roligo = it->second.reverse; + + //cout << it->first << '\t' << foligo << '\t' << roligo << endl; + //cout << it->first << '\t' << rawSeq.substr(0,foligo.length()) << '\t' << rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length()) << endl; + if(rawSeq.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(rawSeq.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, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) { + group = it->first; + if (!keepForward) { + string trimmedSeq = rawSeq.substr(foligo.length()); //trim forward barcode + seq.setUnaligned(trimmedSeq.substr(0,(trimmedSeq.length()-roligo.length()))); //trim reverse barcode + if(qual.getName() != ""){ + qual.trimQScores(-1, rawSeq.length()-roligo.length()); + qual.trimQScores(foligo.length(), -1); + } + } + 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 > minFGroup; + vector 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 >::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); + 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;isecond); + int tempminFPos = 0; + for(int i=0;i pdiffs) { success = minDiff; } //no good matches + else{ + //check for reverse match + if (alignment != NULL) { delete alignment; } + + if (irprimers.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 > minRGroup; + vector minRPos; + + string rawRSequence = reverseOligo(seq.getUnaligned()); + + for(map >::iterator it=irprimers.begin();it!=irprimers.end();it++){ + string oligo = reverseOligo(it->first); + //cout << "r before = " << reverseOligo(oligo) << '\t' << reverseOligo(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->alignPrimer(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 << "r after = " << reverseOligo(oligo) << '\t' << reverseOligo(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;isecond); + } + + } + + /*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 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 = rawSeq.length() - minRPos[0]; + } + + //we have an acceptable match for the forward and reverse, but do they match? + if (foundMatch) { + if (!keepForward) { + string trimmedSeq = rawSeq.substr(0, rStart); //trim reverse barcode + seq.setUnaligned(trimmedSeq.substr(fStart)); //trim forward barcode + if(qual.getName() != ""){ + qual.trimQScores(-1, rStart); + qual.trimQScores(fStart, -1); + } + } + success = minDiff; + //cout << "primer = " << ipprimers[group].forward << '\t' << ipprimers[group].reverse << endl; + }else { success = pdiffs + 100; } + } + } + + if (alignment != NULL) { delete alignment; } + } + + return success; + + } + catch(exception& e) { + m->errorOut(e, "TrimOligos", "stripPairedPrimers"); + exit(1); + } + +} + //*******************************************************************/ int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, QualityScores& forwardQual, QualityScores& reverseQual, int& group){ try { @@ -929,7 +1412,7 @@ int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, Quality } //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)); + alignment->alignPrimer(oligo, rawFSequence.substr(0,oligo.length()+pdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -992,7 +1475,7 @@ int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, Quality } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawRSequence.substr(0,oligo.length()+pdiffs)); + alignment->alignPrimer(oligo, rawRSequence.substr(0,oligo.length()+pdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -1156,7 +1639,7 @@ int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, int& gr } //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)); + alignment->alignPrimer(oligo, rawFSequence.substr(0,oligo.length()+pdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -1219,7 +1702,7 @@ int TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq, int& gr } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawRSequence.substr(0,oligo.length()+pdiffs)); + alignment->alignPrimer(oligo, rawRSequence.substr(0,oligo.length()+pdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -1360,7 +1843,7 @@ int TrimOligos::stripBarcode(Sequence& seq, int& group){ } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs)); + alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+bdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -1460,7 +1943,7 @@ int TrimOligos::stripForward(Sequence& seq, int& group){ } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs)); + alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+pdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -1514,6 +1997,9 @@ int TrimOligos::stripForward(Sequence& seq, int& group){ //*******************************************************************/ int TrimOligos::stripForward(Sequence& seq, QualityScores& qual, int& group, bool keepForward){ try { + + if (paired) { int success = stripPairedPrimers(seq, qual, group, keepForward); return success; } + string rawSequence = seq.getUnaligned(); int success = pdiffs + 1; //guilty until proven innocent @@ -1560,7 +2046,7 @@ int TrimOligos::stripForward(Sequence& seq, QualityScores& qual, int& group, boo } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs)); + alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+pdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -1722,7 +2208,7 @@ bool TrimOligos::stripLinker(Sequence& seq, QualityScores& qual){ } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawSequence.substr(0,oligo.length()+ldiffs)); + alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+ldiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -1821,7 +2307,7 @@ bool TrimOligos::stripLinker(Sequence& seq){ } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawSequence.substr(0,oligo.length()+ldiffs)); + alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+ldiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -1918,7 +2404,7 @@ bool TrimOligos::stripSpacer(Sequence& seq, QualityScores& qual){ } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawSequence.substr(0,oligo.length()+sdiffs)); + alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+sdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -2017,7 +2503,7 @@ bool TrimOligos::stripSpacer(Sequence& seq){ } //use needleman to align first barcode.length()+numdiffs of sequence to each barcode - alignment->align(oligo, rawSequence.substr(0,oligo.length()+sdiffs)); + alignment->alignPrimer(oligo, rawSequence.substr(0,oligo.length()+sdiffs)); oligo = alignment->getSeqAAln(); string temp = alignment->getSeqBAln(); @@ -2137,6 +2623,48 @@ int TrimOligos::countDiffs(string oligo, string seq){ exit(1); } } +//********************************************************************/ +string TrimOligos::reverseOligo(string oligo){ + try { + string reverse = ""; + + for(int i=oligo.length()-1;i>=0;i--){ + + if(oligo[i] == 'A') { reverse += 'T'; } + else if(oligo[i] == 'T'){ reverse += 'A'; } + else if(oligo[i] == 'U'){ reverse += 'A'; } + + else if(oligo[i] == 'G'){ reverse += 'C'; } + else if(oligo[i] == 'C'){ reverse += 'G'; } + + else if(oligo[i] == 'R'){ reverse += 'Y'; } + else if(oligo[i] == 'Y'){ reverse += 'R'; } + + else if(oligo[i] == 'M'){ reverse += 'K'; } + else if(oligo[i] == 'K'){ reverse += 'M'; } + + else if(oligo[i] == 'W'){ reverse += 'W'; } + else if(oligo[i] == 'S'){ reverse += 'S'; } + + else if(oligo[i] == 'B'){ reverse += 'V'; } + else if(oligo[i] == 'V'){ reverse += 'B'; } + + else if(oligo[i] == 'D'){ reverse += 'H'; } + else if(oligo[i] == 'H'){ reverse += 'D'; } + + else if(oligo[i] == '-'){ reverse += '-'; } + else { reverse += 'N'; } + } + + + return reverse; + } + catch(exception& e) { + m->errorOut(e, "TrimOligos", "reverseOligo"); + exit(1); + } +} + /********************************************************************/