/********************************************************************/
TrimOligos::~TrimOligos() {}
//*******************************************************************/
int TrimOligos::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
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()));
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
int maxLength = 0;
Alignment* alignment;
if (barcodes.size() > 0) {
map<string,int>::iterator it=barcodes.begin();
for(it;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; }
//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() < maxLength){ //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, 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));
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);
}
}
//*******************************************************************/
int TrimOligos::stripBarcode(Sequence& seq, int& group){
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
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; }
//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() < maxLength){ //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, 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);
}
}
//********************************************************************/
int TrimOligos::stripForward(Sequence& seq, int& group){
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
int maxLength = 0;
Alignment* alignment;
if (primers.size() > 0) {
map<string,int>::iterator it=primers.begin();
for(it;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; }
//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() < maxLength){
success = pdiffs + 100;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
alignment->align(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);
}
}
//*******************************************************************/
int TrimOligos::stripForward(Sequence& seq, QualityScores& qual, int& group){
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()));
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 ((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=primers.begin();
for(it;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; }
//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() < maxLength){
success = pdiffs + 100;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
alignment->align(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));
if(qual.getName() != ""){
qual.trimQScores(minPos, -1);
}
success = minDiff;
}
if (alignment != NULL) { delete alignment; }
}
return success;
}
catch(exception& e) {
m->errorOut(e, "TrimOligos", "stripForward");
exit(1);
}
}
//******************************************************************/
bool TrimOligos::stripReverse(Sequence& seq, QualityScores& qual){
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);
}
}
/********************************************************************/
TrimOligos::~TrimOligos() {}
//*******************************************************************/
int TrimOligos::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
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()));
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
int maxLength = 0;
Alignment* alignment;
if (barcodes.size() > 0) {
map<string,int>::iterator it=barcodes.begin();
for(it;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; }
//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() < maxLength){ //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, 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));
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);
}
}
//*******************************************************************/
int TrimOligos::stripBarcode(Sequence& seq, int& group){
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
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; }
//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() < maxLength){ //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, 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);
}
}
//********************************************************************/
int TrimOligos::stripForward(Sequence& seq, int& group){
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
int maxLength = 0;
Alignment* alignment;
if (primers.size() > 0) {
map<string,int>::iterator it=primers.begin();
for(it;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; }
//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() < maxLength){
success = pdiffs + 100;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
alignment->align(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);
}
}
//*******************************************************************/
int TrimOligos::stripForward(Sequence& seq, QualityScores& qual, int& group){
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()));
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 ((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=primers.begin();
for(it;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; }
//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() < maxLength){
success = pdiffs + 100;
break;
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
alignment->align(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));
if(qual.getName() != ""){
qual.trimQScores(minPos, -1);
}
success = minDiff;
}
if (alignment != NULL) { delete alignment; }
}
return success;
}
catch(exception& e) {
m->errorOut(e, "TrimOligos", "stripForward");
exit(1);
}
}
