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|
//
// oligos.cpp
// Mothur
//
// Created by Sarah Westcott on 4/4/14.
// Copyright (c) 2014 Schloss Lab. All rights reserved.
//
#include "oligos.h"
#include "utils.hpp"
/**************************************************************************************************/
Oligos::Oligos(string o){
try {
m = MothurOut::getInstance();
hasPPrimers = false; hasPBarcodes = false; pairedOligos = false; reversePairs = true;
indexBarcode = 0; indexPairedBarcode = 0; indexPrimer = 0; indexPairedPrimer = 0;
oligosfile = o;
reversePairs = true;
readOligos();
if (pairedOligos) {
numBarcodes = pairedBarcodes.size();
numFPrimers = pairedPrimers.size();
}else {
numBarcodes = barcodes.size();
numFPrimers = primers.size();
}
}
catch(exception& e) {
m->errorOut(e, "Oligos", "Oligos");
exit(1);
}
}
/**************************************************************************************************/
Oligos::Oligos(){
try {
m = MothurOut::getInstance();
hasPPrimers = false; hasPBarcodes = false; pairedOligos = false; reversePairs = true;
indexBarcode = 0; indexPairedBarcode = 0; indexPrimer = 0; indexPairedPrimer = 0;
numFPrimers = 0; numBarcodes = 0;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "Oligos");
exit(1);
}
}
/**************************************************************************************************/
int Oligos::read(string o){
try {
oligosfile = o;
readOligos();
if (pairedOligos) {
numBarcodes = pairedBarcodes.size();
numFPrimers = pairedPrimers.size();
}else {
numBarcodes = barcodes.size();
numFPrimers = primers.size();
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "read");
exit(1);
}
}
/**************************************************************************************************/
int Oligos::read(string o, bool reverse){
try {
oligosfile = o;
reversePairs = reverse;
readOligos();
if (pairedOligos) {
numBarcodes = pairedBarcodes.size();
numFPrimers = pairedPrimers.size();
}else {
numBarcodes = barcodes.size();
numFPrimers = primers.size();
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "read");
exit(1);
}
}
/**************************************************************************************************/
vector<string> Oligos::getSRAGroupNames(){
try {
vector<string> sraGroupNames;
set<string> uniqueNames;
if (pairedOligos) {
for(map<int, oligosPair>::iterator itBar = pairedBarcodes.begin();itBar != pairedBarcodes.end();itBar++){
for(map<int, oligosPair>::iterator itPrimer = pairedPrimers.begin();itPrimer != pairedPrimers.end(); itPrimer++){
if (m->getControl_pressed()) { return sraGroupNames; }
string primerName = getPrimerName(itPrimer->first);
string barcodeName = getBarcodeName(itBar->first);
if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
else if ((primerName == "") && (barcodeName == "")) { } //do nothing
else {
string comboGroupName = "";
string comboName = "";
if(primerName == ""){
comboGroupName = barcodeName;
}else{
if(barcodeName == ""){
comboGroupName = primerName;
}
else{
comboGroupName = barcodeName + "." + primerName;
}
}
if(((itPrimer->second).forward+(itPrimer->second).reverse) == ""){
if ((itBar->second).forward != "NONE") { comboName += (itBar->second).forward; }
if ((itBar->second).reverse != "NONE") {
if (comboName == "") { comboName += (itBar->second).reverse; }
else { comboName += ("."+(itBar->second).reverse); }
}
}else{
if(((itBar->second).forward+(itBar->second).reverse) == ""){
if ((itPrimer->second).forward != "NONE") { comboName += (itPrimer->second).forward; }
if ((itPrimer->second).reverse != "NONE") {
if (comboName == "") { comboName += (itPrimer->second).reverse; }
else { comboName += ("."+(itPrimer->second).reverse); }
}
}
else{
if ((itBar->second).forward != "NONE") { comboName += (itBar->second).forward; }
if ((itBar->second).reverse != "NONE") {
if (comboName == "") { comboName += (itBar->second).reverse; }
else { comboName += ("."+(itBar->second).reverse); }
}
if ((itPrimer->second).forward != "NONE") {
if (comboName == "") { comboName += (itPrimer->second).forward; }
else { comboName += ("."+(itPrimer->second).forward); }
}
if ((itPrimer->second).reverse != "NONE") {
if (comboName == "") { comboName += (itPrimer->second).reverse; }
else { comboName += ("."+(itPrimer->second).reverse); }
}
}
}
if (comboName != "") { comboGroupName += "_" + comboName; }
uniqueNames.insert(comboGroupName);
}
}
}
}else {
for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
string primerName = getPrimerName(itPrimer->second);
string barcodeName = getBarcodeName(itBar->second);
if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
else if ((primerName == "") && (barcodeName == "")) { } //do nothing
else {
string comboGroupName = "";
string comboName = "";
if(primerName == ""){
comboGroupName = barcodeName;
}else{
if(barcodeName == ""){
comboGroupName = primerName;
}
else{
comboGroupName = barcodeName + "." + primerName;
}
}
if(itPrimer->first == ""){
comboName = itBar->first;
}else{
if(itBar->first == ""){
comboName = itPrimer->first;
}
else{
comboName = itBar->first + "." + itPrimer->first;
}
}
if (comboName != "") { comboGroupName += "_" + comboName; }
uniqueNames.insert(comboGroupName);
}
}
}
}
if (uniqueNames.size() == 0) {
m->mothurOut("[ERROR]: your oligos file does not contain any group names.\n"); m->setControl_pressed(true);
}else {
if (m->getDebug()) { int count = 0; for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { m->mothurOut("[DEBUG]: " + toString(count) + " groupName = " + *it + "\n"); count++; } }
for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { sraGroupNames.push_back(*it); }
}
return sraGroupNames;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getSRAGroupNames");
exit(1);
}
}
//***************************************************************************************************************
int Oligos::readOligos(){
try {
ifstream inOligos;
Utils util; util.openInputFile(oligosfile, inOligos);
string type, oligo, roligo, group;
bool pfUsesNone = false; bool prUsesNone = false; bool bfUsesNone = false; bool brUsesNone = false;
set<string> uniqueBarcodes;
set<string> uniquePrimers;
while(!inOligos.eof()){
string line = util.getline(inOligos); gobble(inOligos);
if(line[0] == '#'){} //ignore
else{
vector<string> pieces = util.splitWhiteSpace(line);
toUpper(pieces[0]); type = pieces[0];//make type case insensitive
oligo = pieces[1]; formatOligo(oligo);
if (m->getDebug()) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); }
if(type == "FORWARD"){
group = "";
if (pieces.size() > 2) { group = pieces[2]; }
//check for repeat primers
map<string, int>::iterator itPrime = primers.find(oligo);
if (itPrime != primers.end()) { m->mothurOut("[WARNING]: primer " + oligo + " is in your oligos file already, disregarding.\n"); }
else {
if (m->getDebug()) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer " + oligo + ".\n"); } }
primers[oligo]=indexPrimer; indexPrimer++;
primerNameVector.push_back(group);
}
}
else if (type == "PRIMER"){
roligo = pieces[2]; formatOligo(roligo);
if (oligo == "NONE") { pfUsesNone = true; }
else if (roligo == "NONE") { prUsesNone = true; }
if (roligo != "NONE") {
if (reversePairs) { roligo = reverseOligo(roligo); }
}
group = "";
if (pieces.size() > 3) { group = pieces[3]; }
oligosPair newPrimer(oligo, roligo);
if (m->getDebug()) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
//check for repeat barcodes
string tempPair = oligo+roligo;
if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("[WARNING]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already, disregarding.\n"); }
else { uniquePrimers.insert(tempPair);
if (m->getDebug()) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); } }
pairedPrimers[indexPairedPrimer]=newPrimer; indexPairedPrimer++;
primerNameVector.push_back(group);
hasPPrimers = true;
}
}
else if(type == "REVERSE"){
string oligoRC = reverseOligo(oligo);
revPrimer.push_back(oligoRC);
}
else if(type == "BARCODE"){
//barcode lines can look like BARCODE atgcatgc groupName - for 454 seqs
//or BARCODE atgcatgc atgcatgc groupName - for illumina data that has forward and reverse info
group = "";
if (pieces.size() == 3) {
group = pieces[2];
//check for repeat barcodes
map<string, int>::iterator itBar = barcodes.find(oligo);
if (itBar != barcodes.end()) { m->mothurOut("[WARNING]: barcode " + oligo + " is in your oligos file already, disregarding.\n"); }
else {
barcodes[oligo]=indexBarcode; indexBarcode++;
barcodeNameVector.push_back(group);
}
}
else if (pieces.size() == 4) {
hasPBarcodes = true;
string reverseBarcode = pieces[2]; formatOligo(reverseBarcode);
group = pieces[3];
if (oligo == "NONE") { bfUsesNone = true; }
else if (reverseBarcode == "NONE") { brUsesNone = true; }
if (reverseBarcode != "NONE") {
if (reversePairs) { reverseBarcode = reverseOligo(reverseBarcode); }
}
oligosPair newPair(oligo, reverseBarcode);
if (m->getDebug()) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
//check for repeat barcodes
string tempPair = oligo+reverseBarcode;
if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse + " is in your oligos file already, disregarding.\n"); }
else {
uniqueBarcodes.insert(tempPair);
pairedBarcodes[indexPairedBarcode]=newPair; indexPairedBarcode++;
barcodeNameVector.push_back(group);
}
}
}else if(type == "LINKER"){
linker.push_back(oligo);
}else if(type == "SPACER"){
spacer.push_back(oligo);
}
else{ m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are primer, forward, reverse, and barcode. Ignoring " + oligo + ".\n"); }
}
}
inOligos.close();
if ((linker.size() == 0) && (spacer.size() == 0) && (pairedBarcodes.size() == 0) && (barcodes.size() == 0) && (pairedPrimers.size() == 0) && (primers.size() == 0) && (revPrimer.size() == 0)) { m->mothurOut("[ERROR]: invalid oligos file, quitting.\n"); m->setControl_pressed(true); return 0; }
if (hasPBarcodes || hasPPrimers) {
pairedOligos = true;
if ((primers.size() != 0) || (barcodes.size() != 0) || (linker.size() != 0) || (spacer.size() != 0) || (revPrimer.size() != 0)) { m->setControl_pressed(true); m->mothurOut("[ERROR]: cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting.\n"); return 0; }
//check for "NONE" to make sure if none is used then all primers in that position are NONE
//ex. Can't have: PRIMER NONE reversePrimer and PRIMER fowardPrimer reversePrimer in same file
if (bfUsesNone) {
bool allNONE = true;
for(map<int, oligosPair>::iterator itBar = pairedBarcodes.begin();itBar != pairedBarcodes.end();itBar++){
if ((itBar->second).forward != "NONE") {
allNONE = false;
break;
}
}
if (!allNONE) {
m->setControl_pressed(true); m->mothurOut("[ERROR]: cannot mix forwardBarcode=NONE and forwardBarcode=barcodeString in same file. Mothur assumes all sequences have forward barcodes or all do not, quitting.\n"); return 0;
}
}
if (brUsesNone) {
bool allNONE = true;
for(map<int, oligosPair>::iterator itBar = pairedBarcodes.begin();itBar != pairedBarcodes.end();itBar++){
if ((itBar->second).reverse != "NONE") {
allNONE = false;
break;
}
}
if (!allNONE) {
m->setControl_pressed(true); m->mothurOut("[ERROR]: cannot mix reverseBarcode=NONE and reverseBarcode=barcodeString in same file. Mothur assumes all sequences have reverse barcodes or all do not, quitting.\n"); return 0;
}
}
if (pfUsesNone) {
bool allNONE = true;
for(map<int, oligosPair>::iterator itPrimer = pairedPrimers.begin();itPrimer != pairedPrimers.end(); itPrimer++){
if ((itPrimer->second).forward != "NONE") {
allNONE = false;
break;
}
}
if (!allNONE) {
m->setControl_pressed(true); m->mothurOut("[ERROR]: cannot mix forwardPrimer=NONE and forwardPrimer=primerString in same file. Mothur assumes all sequences have forward primers or all do not, quitting.\n"); return 0;
}
}
if (prUsesNone) {
bool allNONE = true;
for(map<int, oligosPair>::iterator itPrimer = pairedPrimers.begin();itPrimer != pairedPrimers.end(); itPrimer++){
if ((itPrimer->second).reverse != "NONE") {
allNONE = false;
break;
}
}
if (!allNONE) {
m->setControl_pressed(true); m->mothurOut("[ERROR]: cannot mix reversePrimer=NONE and reversePrimer=primerString in same file. Mothur assumes all sequences have reverse primers or all do not, quitting.\n"); return 0;
}
}
}
//add in potential combos
if(barcodeNameVector.size() == 0){
if (pairedOligos) {
oligosPair newPair("", "");
pairedBarcodes[0] = newPair;
}else {
barcodes[""] = 0;
}
barcodeNameVector.push_back("");
}
if(primerNameVector.size() == 0){
if (pairedOligos) {
oligosPair newPair("", "");
pairedPrimers[0] = newPair;
}else {
primers[""] = 0;
}
primerNameVector.push_back("");
}
if (pairedOligos) {
for(map<int, oligosPair>::iterator itBar = pairedBarcodes.begin();itBar != pairedBarcodes.end();itBar++){
for(map<int, oligosPair>::iterator itPrimer = pairedPrimers.begin();itPrimer != pairedPrimers.end(); itPrimer++){
string primerName = primerNameVector[itPrimer->first];
string barcodeName = barcodeNameVector[itBar->first];
if (m->getDebug()) { m->mothurOut("[DEBUG]: primerName = " + primerName + " barcodeName = " + barcodeName + "\n"); }
if ((primerName == "ignore") || (barcodeName == "ignore")) { if (m->getDebug()) { m->mothurOut("[DEBUG]: in ignore. \n"); } } //do nothing
else if ((primerName == "") && (barcodeName == "")) { if (m->getDebug()) { m->mothurOut("[DEBUG]: in blank. \n"); } } //do nothing
else {
string comboGroupName = "";
string fastqFileName = "";
if(primerName == ""){
comboGroupName = barcodeNameVector[itBar->first];
}else{
if(barcodeName == ""){
comboGroupName = primerNameVector[itPrimer->first];
}
else{
comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
}
}
if (m->getDebug()) { m->mothurOut("[DEBUG]: comboGroupName = " + comboGroupName + "\n"); }
uniqueNames.insert(comboGroupName);
map<string, vector<string> >::iterator itGroup2Barcode = Group2Barcode.find(comboGroupName);
if (itGroup2Barcode == Group2Barcode.end()) {
vector<string> tempBarcodes; tempBarcodes.push_back((itBar->second).forward+"."+(itBar->second).reverse);
Group2Barcode[comboGroupName] = tempBarcodes;
}else {
Group2Barcode[comboGroupName].push_back((itBar->second).forward+"."+(itBar->second).reverse);
}
itGroup2Barcode = Group2Primer.find(comboGroupName);
if (itGroup2Barcode == Group2Primer.end()) {
vector<string> tempPrimers; tempPrimers.push_back((itPrimer->second).forward+"."+(itPrimer->second).reverse);
Group2Primer[comboGroupName] = tempPrimers;
}else {
Group2Primer[comboGroupName].push_back((itPrimer->second).forward+"."+(itPrimer->second).reverse);
}
}
}
}
}else {
for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
string primerName = primerNameVector[itPrimer->second];
string barcodeName = barcodeNameVector[itBar->second];
if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
else if ((primerName == "") && (barcodeName == "")) { } //do nothing
else {
string comboGroupName = "";
string fastqFileName = "";
if(primerName == ""){
comboGroupName = barcodeNameVector[itBar->second];
}
else{
if(barcodeName == ""){
comboGroupName = primerNameVector[itPrimer->second];
}
else{
comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
}
}
uniqueNames.insert(comboGroupName);
map<string, vector<string> >::iterator itGroup2Barcode = Group2Barcode.find(comboGroupName);
if (itGroup2Barcode == Group2Barcode.end()) {
vector<string> tempBarcodes; tempBarcodes.push_back(itBar->first);
Group2Barcode[comboGroupName] = tempBarcodes;
}else {
Group2Barcode[comboGroupName].push_back(itBar->first);
}
itGroup2Barcode = Group2Primer.find(comboGroupName);
if (itGroup2Barcode == Group2Primer.end()) {
vector<string> tempPrimers; tempPrimers.push_back(itPrimer->first);
Group2Primer[comboGroupName] = tempPrimers;
}else {
Group2Primer[comboGroupName].push_back(itPrimer->first);
}
}
}
}
}
if (m->getDebug()) { int count = 0; for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { m->mothurOut("[DEBUG]: " + toString(count) + " groupName = " + *it + "\n"); count++; } }
Groups.clear();
for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { Groups.push_back(*it); }
return 0;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "readOligos");
exit(1);
}
}
//********************************************************************/
vector<string> Oligos::getBarcodes(string groupName){
try {
vector<string> thisGroupsBarcodes;
map<string, vector<string> >::iterator it = Group2Barcode.find(groupName);
if (it == Group2Barcode.end()) { m->mothurOut("[ERROR]: no barcodes found for group " + groupName + ".\n"); m->setControl_pressed(true);
}else { thisGroupsBarcodes = it->second; }
return thisGroupsBarcodes;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getBarcodes");
exit(1);
}
}
//********************************************************************/
vector<string> Oligos::getPrimers(string groupName){
try {
vector<string> thisGroupsPrimers;
map<string, vector<string> >::iterator it = Group2Primer.find(groupName);
if (it == Group2Primer.end()) { m->mothurOut("[ERROR]: no primers found for group " + groupName + ".\n"); m->setControl_pressed(true);
}else { thisGroupsPrimers = it->second; }
return thisGroupsPrimers;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getPrimers");
exit(1);
}
}
//********************************************************************/
//can't have paired and unpaired so this function will either run the paired map or the unpaired
map<int, oligosPair> Oligos::getReversedPairedPrimers(){
try {
map<int, oligosPair> rpairedPrimers;
set<string> uniquePrimers;
for (map<int, oligosPair>::iterator it = pairedPrimers.begin(); it != pairedPrimers.end(); it++) {
//add reverse compliment barcodes
string forward = reverseOligo((it->second).forward);
string reverse = reverseOligo((it->second).reverse);
string temp = forward+reverse;
if (uniquePrimers.count(temp) != 0) { } //already have this pair assigned to a sample, ignore reversed version
else {
uniquePrimers.insert(temp);
oligosPair tempPair(forward, reverse); //reverseforward, reverseReverse
rpairedPrimers[it->first] = tempPair;
}
}
for (map<string, int>::iterator it = primers.begin(); it != primers.end(); it++) {
//add reverse compliment barcodes
string forward = reverseOligo(it->first);
string reverse = "";
string temp = forward+reverse;
if (uniquePrimers.count(temp) != 0) { } //already have this pair assigned to a sample, ignore reversed version
else {
uniquePrimers.insert(temp);
oligosPair tempPair(forward, reverse); //reverseforward, reverseReverse
rpairedPrimers[it->second] = tempPair;
}
}
return rpairedPrimers;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getReversedPairedPrimers");
exit(1);
}
}
//********************************************************************/
//can't have paired and unpaired so this function will either run the paired map or the unpaired
map<int, oligosPair> Oligos::getReorientedPairedPrimers(){
try {
map<int, oligosPair> rpairedPrimers;
set<string> uniquePrimers;
for (map<int, oligosPair>::iterator it = pairedPrimers.begin(); it != pairedPrimers.end(); it++) {
string forward = (it->second).reverse;
if (reversePairs) { forward = reverseOligo(forward); }
string reverse = (it->second).forward;
if (reversePairs) { reverse = reverseOligo(reverse); }
oligosPair tempPair(forward, reverse); //reversePrimer, rc ForwardPrimer
rpairedPrimers[it->first] = tempPair;
}
for (map<string, int>::iterator it = primers.begin(); it != primers.end(); it++) {
oligosPair tempPair("", reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode
rpairedPrimers[it->second] = tempPair;
}
return rpairedPrimers;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getReorientedPairedPrimers");
exit(1);
}
}
//********************************************************************/
vector<string> Oligos::getReorientedReversePrimers(){
try {
vector<string> revReorientedPrimers;
for (map<string, int>::iterator it = primers.begin(); it != primers.end(); it++) {
string reverse = reverseOligo((it->first)); //rc ForwardPrimer
revReorientedPrimers.push_back(reverse);
}
return revReorientedPrimers;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getReorientedPairedPrimers");
exit(1);
}
}
//********************************************************************/
map<string, int> Oligos::getReorientedPrimers(){
try {
map<string, int> reorientedPrimers;
for (int i = 0; i < revPrimer.size(); i++) {
string primer = reverseOligo(revPrimer[i]);
reorientedPrimers[primer] = -1; //ignore value
}
return reorientedPrimers;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getReorientedPrimers");
exit(1);
}
}
//********************************************************************/
vector<string> Oligos::getReversedReversePrimers(){
try {
vector<string> revReversedPrimers;
for (int i = 0; i < revPrimer.size(); i++) {
string primer = reverseOligo(revPrimer[i]);
revReversedPrimers.push_back(primer);
}
return revReversedPrimers;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getReorientedPairedPrimers");
exit(1);
}
}
//********************************************************************/
map<string, int> Oligos::getReversedPrimers(){
try {
map<string, int> revReversedPrimers;
for (map<string, int>::iterator it = primers.begin(); it != primers.end(); it++) {
string reverse = reverseOligo((it->first)); //rc ForwardPrimer
revReversedPrimers[reverse] = it->second;
}
return revReversedPrimers;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getReorientedPrimers");
exit(1);
}
}
//********************************************************************/
//can't have paired and unpaired so this function will either run the paired map or the unpaired
map<int, oligosPair> Oligos::getReversedPairedBarcodes(){
try {
map<int, oligosPair> rpairedBarcodes;
set<string> uniqueBarcodes;
for (map<int, oligosPair>::iterator it = pairedBarcodes.begin(); it != pairedBarcodes.end(); it++) {
//add reverse compliment barcodes
string forward = reverseOligo((it->second).forward);
string reverse = reverseOligo((it->second).reverse);
string temp = forward+reverse;
if (uniqueBarcodes.count(temp) != 0) { } //already have this pair assigned to a sample, ignore reversed version
else {
uniqueBarcodes.insert(temp);
oligosPair tempPair(forward, reverse); //reverseforward, reverseReverse
rpairedBarcodes[it->first] = tempPair;
}
}
for (map<string, int>::iterator it = barcodes.begin(); it != barcodes.end(); it++) {
//add reverse compliment barcodes
string forward = reverseOligo(it->first);
string reverse = "";
string temp = forward+reverse;
if (uniqueBarcodes.count(temp) != 0) { } //already have this pair assigned to a sample, ignore reversed version
else {
uniqueBarcodes.insert(temp);
oligosPair tempPair(forward, reverse); //reverseforward, reverseReverse
rpairedBarcodes[it->second] = tempPair;
}
}
return rpairedBarcodes;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getReversedPairedBarcodes");
exit(1);
}
}
//********************************************************************/
//can't have paired and unpaired so this function will either run the paired map or the unpaired
map<int, oligosPair> Oligos::getReorientedPairedBarcodes(){
try {
map<int, oligosPair> rpairedBarcodes;
set<string> uniqueBarcodes;
for (map<int, oligosPair>::iterator it = pairedBarcodes.begin(); it != pairedBarcodes.end(); it++) {
string forward = (it->second).reverse;
if (reversePairs) { forward = reverseOligo(forward); } //forward is now the reverse of reverse
string reverse = (it->second).forward;
if (reversePairs) { reverse = reverseOligo(reverse); } //reverse is now the reverse of forward
//check for repeat barcodes
string temp = forward+reverse;
if (uniqueBarcodes.count(temp) != 0) { } //already have this pair assigned to a sample, ignore reoriented version
else {
uniqueBarcodes.insert(temp);
oligosPair tempPair(forward, reverse); //(reverse, forward) or if reversePairs (rc_reverse, rc_forward)
rpairedBarcodes[it->first] = tempPair;
}
}
for (map<string, int>::iterator it = barcodes.begin(); it != barcodes.end(); it++) {
string forward = ""; string reverse = reverseOligo((it->first));
string temp = forward+reverse;
if (uniqueBarcodes.count(temp) != 0) { } //already have this pair assigned to a sample, ignore reoriented version
else { uniqueBarcodes.insert(temp);
oligosPair tempPair(forward, reverse); //reversePrimer, rc ForwardPrimer
rpairedBarcodes[it->second] = tempPair;
}
}
return rpairedBarcodes;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getReorientedPairedBarcodes");
exit(1);
}
}
//********************************************************************/
string Oligos::reverseOligo(string oligo){
try {
if (oligo == "NONE") { return "NONE"; }
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 { reverse += 'N'; }
}
return reverse;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "reverseOligo");
exit(1);
}
}
//********************************************************************/
void Oligos::formatOligo(string& oligo){
try {
for(int i=0;i<oligo.length();i++){
oligo[i] = toupper(oligo[i]);
if(oligo[i] == 'U') { oligo[i] = 'T'; }
}
}
catch(exception& e) {
m->errorOut(e, "Oligos", "formatOligo");
exit(1);
}
}
//********************************************************************/
string Oligos::getBarcodeName(int index){
try {
string name = "";
if ((index >= 0) && (index < barcodeNameVector.size())) { name = barcodeNameVector[index]; }
return name;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getBarcodeName");
exit(1);
}
}
//********************************************************************/
string Oligos::getPrimerName(int index){
try {
string name = "";
if ((index >= 0) && (index < primerNameVector.size())) { name = primerNameVector[index]; }
return name;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getPrimerName");
exit(1);
}
}
//********************************************************************/
string Oligos::getGroupName(int barcodeIndex, int primerIndex){
try {
string thisGroup = "";
if(numBarcodes != 0){
thisGroup = getBarcodeName(barcodeIndex);
if (numFPrimers != 0) {
if (getPrimerName(primerIndex) != "") {
if(thisGroup != "") {
thisGroup += "." + getPrimerName(primerIndex);
}else {
thisGroup = getPrimerName(primerIndex);
}
}
}
}
return thisGroup;
}
catch(exception& e) {
m->errorOut(e, "Oligos", "getGroupName");
exit(1);
}
}
/**************************************************************************************************/
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