CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
-
+ CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient);
CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "","",false,false); parameters.push_back(palign);
CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pallfiles);
CommandParameter ptrimoverlap("trimoverlap", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptrimoverlap);
//helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n";
+ helpString += "The checkorient parameter will check look for the reverse compliment of the barcode or primer in the sequence. If found the sequence is flipped. The default is false.\n";
helpString += "The deltaq parameter allows you to specify the delta allowed between quality scores of a mismatched base. For example in the overlap, if deltaq=5 and in the alignment seqA, pos 200 has a quality score of 30 and the same position in seqB has a quality score of 20, you take the base from seqA (30-20 >= 5). If the quality score in seqB is 28 then the base in the consensus will be an N (30-28<5) The default is 6.\n";
helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n";
//if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
abort=true;
}
+ temp = validParameter.validFile(parameters, "checkorient", false); if (temp == "not found") { temp = "F"; }
+ reorient = m->isTrue(temp);
+
//fill convert table - goes from solexa to sanger. Used fq_all2std.pl as a reference.
for (int i = -64; i < 65; i++) {
char temp = (char) ((int)(33 + 10*log(1+pow(10,(i/10.0)))/log(10)+0.499));
groupCounts.clear();
groupMap.clear();
vector<vector<string> > fastaFileNames;
+ map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
createOligosGroup = false;
+ oligos = new Oligos();
+ numBarcodes = 0; numFPrimers= 0; numLinkers= 0; numSpacers = 0; numRPrimers = 0;
string outputGroupFileName;
map<string, string> variables;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir = m->hasPath(filesToProcess[l][0][0]); }
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(filesToProcess[l][0][0]));
variables["[tag]"] = "";
- if(oligosfile != ""){ createOligosGroup = getOligos(fastaFileNames, variables["[filename]"]); }
+ if(oligosfile != ""){ createOligosGroup = getOligos(fastaFileNames, variables["[filename]"], uniqueFastaNames); }
if (createOligosGroup || createFileGroup) {
outputGroupFileName = getOutputFileName("group",variables);
}
//remove temp fasta and qual files
for (int i = 0; i < processors; i++) { for(int j = 0; j < filesToProcess[l][i].size(); j++) { m->mothurRemove(filesToProcess[l][i][j]); } }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete oligos; return 0; }
if(allFiles){
- map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
+ // so we don't add the same groupfile multiple times
map<string, string>::iterator it;
set<string> namesToRemove;
for(int i=0;i<fastaFileNames.size();i++){
if(m->isBlank(fastaFileNames[i][j])){
m->mothurRemove(fastaFileNames[i][j]);
namesToRemove.insert(fastaFileNames[i][j]);
- }else{
- it = uniqueFastaNames.find(fastaFileNames[i][j]);
- if (it == uniqueFastaNames.end()) {
- uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
- }
+ uniqueFastaNames.erase(fastaFileNames[i][j]); //remove from list for group file print
}
}
}
m->openInputFile(it->first, in);
ofstream out;
- string thisGroupName = thisOutputDir + m->getRootName(m->getSimpleName(it->first));
- thisGroupName += getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(it->first));
+ string thisGroupName = getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
m->openOutputFile(thisGroupName, out);
while (!in.eof()){
}
}
m->mothurOut("Done.\n");
+ delete oligos;
}
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
}
}
- contigsData* tempcontig = new contigsData(group, files[h], (outputFasta + extension), (outputScrapFasta + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, insert, deltaq, barcodes, primers, tempFASTAFileNames, barcodeNameVector, primerNameVector, pdiffs, bdiffs, tdiffs, createOligosGroup, createFileGroup, allFiles, trimOverlap, h);
+ contigsData* tempcontig = new contigsData(group, files[h], (outputFasta + extension), (outputScrapFasta + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, insert, deltaq, tempFASTAFileNames, oligosfile, reorient, pdiffs, bdiffs, tdiffs, createOligosGroup, createFileGroup, allFiles, trimOverlap, h);
pDataArray.push_back(tempcontig);
hThreadArray[h] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
m->openOutputFile(outputMisMatches, outMisMatch);
outMisMatch << "Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns\n";
- TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, primers, barcodes);
+ TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, oligos->getPairedPrimers(), oligos->getPairedBarcodes());
+
+ TrimOligos* rtrimOligos = NULL;
+ if (reorient) {
+ rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligos->getReorientedPairedPrimers(), oligos->getReorientedPairedBarcodes()); numBarcodes = oligos->getReorientedPairedBarcodes().size();
+ }
while ((!inFFasta.eof()) && (!inRFasta.eof())) {
int barcodeIndex = 0;
int primerIndex = 0;
+ Sequence savedFSeq(fSeq.getName(), fSeq.getAligned()); Sequence savedRSeq(rSeq.getName(), rSeq.getAligned());
+ Sequence savedFindex(findexBarcode.getName(), findexBarcode.getAligned()); Sequence savedRIndex(rindexBarcode.getName(), rindexBarcode.getAligned());
+ QualityScores* savedFQual = NULL; QualityScores* savedRQual = NULL;
+ if (thisfqualfile != "") {
+ savedFQual = new QualityScores(fQual->getName(), fQual->getQualityScores());
+ savedRQual = new QualityScores(rQual->getName(), rQual->getQualityScores());
+ }
- if(barcodes.size() != 0){
+ if(numBarcodes != 0){
if (thisfqualfile != "") {
if ((thisfindexfile != "") || (thisrindexfile != "")) {
success = trimOligos.stripBarcode(findexBarcode, rindexBarcode, *fQual, *rQual, barcodeIndex);
else{ currentSeqsDiffs += success; }
}
- if(primers.size() != 0){
+ if(numFPrimers != 0){
if (thisfqualfile != "") {
success = trimOligos.stripForward(fSeq, rSeq, *fQual, *rQual, primerIndex);
}else {
if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
+ if (reorient && (trashCode != "")) { //if you failed and want to check the reverse
+ int thisSuccess = 0;
+ string thisTrashCode = "";
+ int thisCurrentSeqsDiffs = 0;
+
+ int thisBarcodeIndex = 0;
+ int thisPrimerIndex = 0;
+
+ if(numBarcodes != 0){
+ if (thisfqualfile != "") {
+ if ((thisfindexfile != "") || (thisrindexfile != "")) {
+ thisSuccess = rtrimOligos->stripBarcode(savedFindex, savedRIndex, *savedFQual, *savedRQual, thisBarcodeIndex);
+ }else {
+ thisSuccess = rtrimOligos->stripBarcode(savedFSeq, savedRSeq, *savedFQual, *savedRQual, thisBarcodeIndex);
+ }
+ }else {
+ thisSuccess = rtrimOligos->stripBarcode(savedFSeq, savedRSeq, thisBarcodeIndex);
+ }
+ if(thisSuccess > bdiffs) { thisTrashCode += 'b'; }
+ else{ thisCurrentSeqsDiffs += thisSuccess; }
+ }
+
+ if(numFPrimers != 0){
+ if (thisfqualfile != "") {
+ thisSuccess = rtrimOligos->stripForward(savedFSeq, savedRSeq, *savedFQual, *savedRQual, thisPrimerIndex);
+ }else {
+ thisSuccess = rtrimOligos->stripForward(savedFSeq, savedRSeq, thisPrimerIndex);
+ }
+ if(thisSuccess > pdiffs) { thisTrashCode += 'f'; }
+ else{ thisCurrentSeqsDiffs += thisSuccess; }
+ }
+
+ if (thisCurrentSeqsDiffs > tdiffs) { thisTrashCode += 't'; }
+
+ if (thisTrashCode == "") {
+ trashCode = thisTrashCode;
+ success = thisSuccess;
+ currentSeqsDiffs = thisCurrentSeqsDiffs;
+ barcodeIndex = thisBarcodeIndex;
+ primerIndex = thisPrimerIndex;
+ savedFSeq.reverseComplement();
+ savedRSeq.reverseComplement();
+ fSeq.setAligned(savedFSeq.getAligned());
+ rSeq.setAligned(savedRSeq.getAligned());
+ if(thisfqualfile != ""){
+ savedFQual->flipQScores(); savedRQual->flipQScores();
+ fQual->setScores(savedFQual->getScores()); rQual->setScores(savedRQual->getScores());
+ }
+ }else { trashCode += "(" + thisTrashCode + ")"; }
+ }
+
+
//flip the reverse reads
rSeq.reverseComplement();
if (thisfqualfile != "") { rQual->flipQScores(); }
if (thisfqualfile != "") {
scores1 = fQual->getQualityScores();
scores2 = rQual->getQualityScores();
- delete fQual; delete rQual;
+ delete fQual; delete rQual; delete savedFQual; delete savedRQual;
}
// if (num < 5) { cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
if (m->debug) { m->mothurOut(fSeq.getName()); }
if (createOligosGroup) {
- if(barcodes.size() != 0){
- string thisGroup = barcodeNameVector[barcodeIndex];
- if (primers.size() != 0) {
- if (primerNameVector[primerIndex] != "") {
- if(thisGroup != "") {
- thisGroup += "." + primerNameVector[primerIndex];
- }else {
- thisGroup = primerNameVector[primerIndex];
- }
- }
- }
-
+ string thisGroup = oligos->getGroupName(barcodeIndex, primerIndex);
if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
int pos = thisGroup.find("ignore");
if (it == groupCounts.end()) { groupCounts[thisGroup] = 1; }
else { groupCounts[it->first] ++; }
}else { ignore = true; }
-
- }
}else if (createFileGroup) {
int pos = group.find("ignore");
if (pos == string::npos) {
}else { ignore = true; }
}
if (m->debug) { m->mothurOut("\n"); }
-
+
if(allFiles && !ignore){
ofstream output;
m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
inRQual.close();
}
delete alignment;
+ if (reorient) { delete rtrimOligos; }
if (m->control_pressed) { m->mothurRemove(outputFasta); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches); }
if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ", forward = " + forward + ", reverse = " + reverse + ", forwardIndex = " + findex + ", reverseIndex = " + rindex + ".\n"); }
+ if (inputDir != "") {
+ string path = m->hasPath(forward);
+ if (path == "") { forward = inputDir + forward; }
+
+ path = m->hasPath(reverse);
+ if (path == "") { reverse = inputDir + reverse; }
+
+ if (findex != "") {
+ path = m->hasPath(findex);
+ if (path == "") { findex = inputDir + findex; }
+ }
+
+ if (rindex != "") {
+ path = m->hasPath(rindex);
+ if (path == "") { rindex = inputDir + rindex; }
+ }
+ }
+
//check to make sure both are able to be opened
ifstream in2;
int openForward = m->openInputFile(forward, in2, "noerror");
//illumina data requires paired forward and reverse data
//BARCODE atgcatgc atgcatgc groupName
//PRIMER atgcatgc atgcatgc groupName
-//PRIMER atgcatgc atgcatgc
-bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, string rootname){
+//PRIMER atgcatgc atgcatgc
+bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, string rootname, map<string, string>& fastaFile2Group){
try {
- ifstream in;
- m->openInputFile(oligosfile, in);
-
- ofstream test;
-
- string type, foligo, roligo, group;
+ if (m->debug) { m->mothurOut("[DEBUG]: oligosfile = " + oligosfile + "\n"); }
- int indexPrimer = 0;
- int indexBarcode = 0;
- set<string> uniquePrimers;
- set<string> uniqueBarcodes;
-
- while(!in.eof()){
-
- in >> type;
+ bool allBlank = false;
+ oligos->read(oligosfile, false);
+
+ if (m->control_pressed) { return false; } //error in reading oligos
+
+ if (oligos->hasPairedBarcodes()) {
+ numFPrimers = oligos->getPairedPrimers().size();
+ numBarcodes = oligos->getPairedBarcodes().size();
+ }else {
+ m->mothurOut("[ERROR]: make.contigs requires paired barcodes and primers. You can set one end to NONE if you are using an index file.\n"); m->control_pressed = true;
+ }
- if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
-
- if(type[0] == '#'){
- while (!in.eof()) { char c = in.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
- m->gobble(in);
- }
- else{
- m->gobble(in);
- //make type case insensitive
- for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
-
- in >> foligo;
-
- if (m->debug) { m->mothurOut("[DEBUG]: reading - " + foligo + ".\n"); }
-
- for(int i=0;i<foligo.length();i++){
- foligo[i] = toupper(foligo[i]);
- if(foligo[i] == 'U') { foligo[i] = 'T'; }
- }
-
- if(type == "PRIMER"){
- m->gobble(in);
-
- in >> roligo;
-
- for(int i=0;i<roligo.length();i++){
- roligo[i] = toupper(roligo[i]);
- if(roligo[i] == 'U') { roligo[i] = 'T'; }
- }
- //roligo = reverseOligo(roligo);
-
- if (m->debug) { m->mothurOut("[DEBUG]: reading - " + roligo + ".\n"); }
-
- group = "";
-
- // get rest of line in case there is a primer name
- while (!in.eof()) {
- char c = in.get();
- if (c == 10 || c == 13 || c == -1){ break; }
- else if (c == 32 || c == 9){;} //space or tab
- else { group += c; }
- }
-
- oligosPair newPrimer(foligo, roligo);
-
- if (m->debug) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
-
- //check for repeat barcodes
- string tempPair = foligo+roligo;
- if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine(); }
- else { uniquePrimers.insert(tempPair); }
-
- if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); } }
- primers[indexPrimer]=newPrimer; indexPrimer++;
- primerNameVector.push_back(group);
- }else if(type == "BARCODE"){
- m->gobble(in);
-
- in >> roligo;
-
- for(int i=0;i<roligo.length();i++){
- roligo[i] = toupper(roligo[i]);
- if(roligo[i] == 'U') { roligo[i] = 'T'; }
- }
- //roligo = reverseOligo(roligo);
-
- oligosPair newPair(foligo, roligo);
-
- if ((foligo == "NONE") || (roligo == "NONE")) { if (!noneOk) { m->mothurOut("[ERROR]: barcodes must be paired unless you are using an index file.\n"); m->control_pressed = true; } }
-
- group = "";
- while (!in.eof()) {
- char c = in.get();
- if (c == 10 || c == 13 || c == -1){ break; }
- else if (c == 32 || c == 9){;} //space or tab
- else { group += c; }
- }
-
- if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
-
- //check for repeat barcodes
- string tempPair = foligo+roligo;
- if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse + " is in your oligos file already, disregarding."); m->mothurOutEndLine(); }
- else { uniqueBarcodes.insert(tempPair); }
-
- barcodes[indexBarcode]=newPair; indexBarcode++;
- barcodeNameVector.push_back(group);
- }else if(type == "LINKER"){
- linker.push_back(foligo);
- m->mothurOut("[WARNING]: make.contigs is not setup to remove linkers, ignoring.\n");
- }else if(type == "SPACER"){
- spacer.push_back(foligo);
- m->mothurOut("[WARNING]: make.contigs is not setup to remove spacers, ignoring.\n");
- }
- else{ m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are primer, barcode, linker and spacer. Ignoring " + foligo + "."); m->mothurOutEndLine(); }
- }
- m->gobble(in);
- }
- in.close();
-
- if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; }
-
- //add in potential combos
- if(barcodeNameVector.size() == 0){
- oligosPair temp("", "");
- barcodes[0] = temp;
- barcodeNameVector.push_back("");
- }
-
- if(primerNameVector.size() == 0){
- oligosPair temp("", "");
- primers[0] = temp;
- primerNameVector.push_back("");
- }
-
- fastaFileNames.resize(barcodeNameVector.size());
+ if (m->control_pressed) { return false; }
+
+ numLinkers = oligos->getLinkers().size();
+ numSpacers = oligos->getSpacers().size();
+ numRPrimers = oligos->getReversePrimers().size();
+ if (numLinkers != 0) { m->mothurOut("[WARNING]: make.contigs is not setup to remove linkers, ignoring.\n"); }
+ if (numSpacers != 0) { m->mothurOut("[WARNING]: make.contigs is not setup to remove spacers, ignoring.\n"); }
+
+ vector<string> groupNames = oligos->getGroupNames();
+ if (groupNames.size() == 0) { allFiles = 0; allBlank = true; }
+
+
+ fastaFileNames.resize(oligos->getBarcodeNames().size());
for(int i=0;i<fastaFileNames.size();i++){
- fastaFileNames[i].assign(primerNameVector.size(), "");
+ for(int j=0;j<oligos->getPrimerNames().size();j++){ fastaFileNames[i].push_back(""); }
}
-
- if(allFiles){
- set<string> uniqueNames; //used to cleanup outputFileNames
- for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
- for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
-
- string primerName = primerNameVector[itPrimer->first];
- string barcodeName = barcodeNameVector[itBar->first];
+
+ if (allFiles) {
+ set<string> uniqueNames; //used to cleanup outputFileNames
+ map<int, oligosPair> barcodes = oligos->getPairedBarcodes();
+ map<int, oligosPair> primers = oligos->getPairedPrimers();
+ for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
+ for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
- if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
- else {
+ string primerName = oligos->getPrimerName(itPrimer->first);
+ string barcodeName = oligos->getBarcodeName(itBar->first);
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { } //do nothing
+ else {
string comboGroupName = "";
string fastaFileName = "";
string qualFileName = "";
string countFileName = "";
if(primerName == ""){
- comboGroupName = barcodeNameVector[itBar->first];
- }
- else{
+ comboGroupName = barcodeName;
+ }else{
if(barcodeName == ""){
- comboGroupName = primerNameVector[itPrimer->first];
+ comboGroupName = primerName;
}
else{
- comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
+ comboGroupName = barcodeName + "." + primerName;
}
}
ofstream temp;
- fastaFileName = rootname + comboGroupName + ".fasta";
+ map<string, string> variables;
+ variables["[filename]"] = rootname;
+ variables["[tag]"] = comboGroupName;
+ fastaFileName = getOutputFileName("fasta", variables);
if (uniqueNames.count(fastaFileName) == 0) {
outputNames.push_back(fastaFileName);
outputTypes["fasta"].push_back(fastaFileName);
uniqueNames.insert(fastaFileName);
+ fastaFile2Group[fastaFileName] = comboGroupName;
}
fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
m->openOutputFile(fastaFileName, temp); temp.close();
+ cout << fastaFileName << endl;
}
- }
- }
- }
-
- bool allBlank = true;
- for (int i = 0; i < barcodeNameVector.size(); i++) {
- if (barcodeNameVector[i] != "") {
- allBlank = false;
- break;
- }
- }
- for (int i = 0; i < primerNameVector.size(); i++) {
- if (primerNameVector[i] != "") {
- allBlank = false;
- break;
- }
- }
-
- if (allBlank) {
- m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile."); m->mothurOutEndLine();
- allFiles = false;
- return false;
- }
-
- return true;
-
+ }
+ }
+ }
+
+ if (allBlank) {
+ m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile."); m->mothurOutEndLine();
+ allFiles = false;
+ return false;
+ }
+
+ return true;
+
}
catch(exception& e) {
m->errorOut(e, "MakeContigsCommand", "getOligos");
exit(1);
}
}
-//********************************************************************/
-string MakeContigsCommand::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 { reverse += 'N'; }
- }
-
-
- return reverse;
- }
- catch(exception& e) {
- m->errorOut(e, "MakeContigsCommand", "reverseOligo");
- exit(1);
- }
-}
//**********************************************************************************************************************
vector<int> MakeContigsCommand::convertQual(string qual) {
try {
vector<int> qualScores;
bool negativeScores = false;
- for (int i = 0; i < qual.length(); i++) {
+ for (int i = 0; i < qual.length(); i++) {
int temp = 0;
temp = int(qual[i]);
projects / mothur.git / blobdiff