#include "trimseqscommand.h"
#include "needlemanoverlap.hpp"
+//**********************************************************************************************************************
+vector<string> TrimSeqsCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
+ "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+TrimSeqsCommand::TrimSeqsCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qual"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> TrimSeqsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> TrimSeqsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//***************************************************************************************************************
TrimSeqsCommand::TrimSeqsCommand(string option) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qual"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+
//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);
if (inputDir == "not found"){ inputDir = ""; }
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("oligos");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["oligos"] = inputDir + it->second; }
}
it = parameters.find("qfile");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["qfile"] = inputDir + it->second; }
}
//check for required parameters
fastaFile = validParameter.validFile(parameters, "fasta", true);
- if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
+ if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the trim.seqs command."); m->mothurOutEndLine(); abort = true; }
else if (fastaFile == "not open") { abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(fastaFile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
}
string temp;
temp = validParameter.validFile(parameters, "flip", false);
if (temp == "not found"){ flip = 0; }
- else if(isTrue(temp)) { flip = 1; }
+ else if(m->isTrue(temp)) { flip = 1; }
temp = validParameter.validFile(parameters, "oligos", true);
if (temp == "not found"){ oligoFile = ""; }
convert(temp, qThreshold);
temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "F"; }
- qtrim = isTrue(temp);
+ qtrim = m->isTrue(temp);
temp = validParameter.validFile(parameters, "rollaverage", false); if (temp == "not found") { temp = "0"; }
convert(temp, qRollAverage);
convert(temp, qAverage);
temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
- allFiles = isTrue(temp);
+ allFiles = m->isTrue(temp);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
convert(temp, processors);
numFPrimers = 0; //this needs to be initialized
numRPrimers = 0;
- string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
- outputNames.push_back(trimSeqFile);
- string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
- outputNames.push_back(scrapSeqFile);
- string trimQualFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.qual";
- outputNames.push_back(trimQualFile);
- string scrapQualFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.qual";
- outputNames.push_back(scrapQualFile);
- string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
+ string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
+ outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
+ string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
+ outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
+ string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
+ string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
+ if (qFileName != "") { outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile); outputTypes["qual"].push_back(trimQualFile); outputTypes["qual"].push_back(scrapQualFile); }
+ string groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
vector<string> fastaFileNames;
vector<string> qualFileNames;
if(oligoFile != ""){
- outputNames.push_back(groupFile);
+ outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
getOligos(fastaFileNames, qualFileNames);
}
//append files
for(int i=1;i<processors;i++){
- appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
+ m->appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
- appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
+ m->appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
- appendFiles((trimQualFile + toString(processIDS[i]) + ".temp"), trimQualFile);
+ m->appendFiles((trimQualFile + toString(processIDS[i]) + ".temp"), trimQualFile);
remove((trimQualFile + toString(processIDS[i]) + ".temp").c_str());
- appendFiles((scrapQualFile + toString(processIDS[i]) + ".temp"), scrapQualFile);
+ m->appendFiles((scrapQualFile + toString(processIDS[i]) + ".temp"), scrapQualFile);
remove((scrapQualFile + toString(processIDS[i]) + ".temp").c_str());
- appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
+ m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
for (int j = 0; j < fastaFileNames.size(); j++) {
- appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
+ m->appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
}
if(qFileName != ""){
for (int j = 0; j < qualFileNames.size(); j++) {
- appendFiles((qualFileNames[j] + toString(processIDS[i]) + ".temp"), qualFileNames[j]);
+ m->appendFiles((qualFileNames[j] + toString(processIDS[i]) + ".temp"), qualFileNames[j]);
remove((qualFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
}
}
if (m->control_pressed) { return 0; }
#else
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qlines[0]);
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
for (int j = 0; j < fastaFileNames.size(); j++) {
rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
for(int i=0;i<fastaFileNames.size();i++){
- if (isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
+ if (m->isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
else {
ifstream inFASTA;
string seqName;
- openInputFile(fastaFileNames[i], inFASTA);
+ m->openInputFile(fastaFileNames[i], inFASTA);
ofstream outGroups;
- string outGroupFilename = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "groups";
- openOutputFile(outGroupFilename, outGroups);
- outputNames.push_back(outGroupFilename);
+ string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
+ m->openOutputFile(outGroupFilename, outGroups);
+ outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);
string thisGroup = "";
if (i > comboStarts) {
if(qFileName != ""){
for(int i=0;i<qualFileNames.size();i++){
- if (isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str()); }
+ if (m->isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str()); }
else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
else {
ifstream inQual;
string seqName;
- openInputFile(qualFileNames[i], inQual);
+ m->openInputFile(qualFileNames[i], inQual);
// ofstream outGroups;
//
// string thisGroup = "";
try {
ofstream outFASTA;
- int able = openOutputFile(trimFile, outFASTA);
+ int able = m->openOutputFile(trimFile, outFASTA);
ofstream scrapFASTA;
- openOutputFile(scrapFile, scrapFASTA);
+ m->openOutputFile(scrapFile, scrapFASTA);
ofstream outQual;
ofstream scrapQual;
if(qFileName != ""){
- openOutputFile(trimQFile, outQual);
- openOutputFile(scrapQFile, scrapQual);
+ m->openOutputFile(trimQFile, outQual);
+ m->openOutputFile(scrapQFile, scrapQual);
}
ofstream outGroups;
- vector<ofstream*> fastaFileNames;
- vector<ofstream*> qualFileNames;
-
+ //vector<ofstream*> fastaFileNames;
+ //vector<ofstream*> qualFileNames;
if (oligoFile != "") {
- openOutputFile(groupFile, outGroups);
+ m->openOutputFile(groupFile, outGroups);
for (int i = 0; i < fastaNames.size(); i++) {
+
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
+ fastaNames[i] = (fastaNames[i] + toString(getpid()) + ".temp");
+ //fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
+ //clear old file if it exists
+ ofstream temp;
+ m->openOutputFile(fastaNames[i], temp);
+ temp.close();
if(qFileName != ""){
- qualFileNames.push_back(new ofstream((qualNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
+ qualNames[i] = (qualNames[i] + toString(getpid()) + ".temp");
+ //qualFileNames.push_back(new ofstream((qualNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
+ //clear old file if it exists
+ ofstream temp2;
+ m->openOutputFile(qualNames[i], temp2);
+ temp2.close();
}
#else
- fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));
+ //fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));
+ fastaNames[i] = (fastaNames[i] + toString(i) + ".temp");
+ ofstream temp;
+ m->openOutputFile(fastaNames[i], temp);
+ temp.close();
if(qFileName != ""){
- qualFileNames.push_back(new ofstream((qualNames[i] + toString(i) + ".temp").c_str(), ios::ate));
+ //qualFileNames.push_back(new ofstream((qualNames[i] + toString(i) + ".temp").c_str(), ios::ate));
+ qualNames[i] = (qualNames[i] + toString(i) + ".temp");
+ ofstream temp2;
+ m->openOutputFile(qualNames[i], temp2);
+ temp2.close();
}
#endif
}
}
ifstream inFASTA;
- openInputFile(filename, inFASTA);
+ m->openInputFile(filename, inFASTA);
inFASTA.seekg(line->start);
ifstream qFile;
- if(qFileName != "") { openInputFile(qFileName, qFile); qFile.seekg(qline->start); }
+ if(qFileName != "") { m->openInputFile(qFileName, qFile); qFile.seekg(qline->start); }
bool done = false;
int count = 0;
inFASTA.close(); outFASTA.close(); scrapFASTA.close();
if (oligoFile != "") { outGroups.close(); }
- for(int i=0;i<fastaFileNames.size();i++){ fastaFileNames[i]->close(); delete fastaFileNames[i]; }
+ //for(int i=0;i<fastaFileNames.size();i++){ fastaFileNames[i]->close(); delete fastaFileNames[i]; }
if(qFileName != ""){
qFile.close();
- for(int i=0;i<qualFileNames.size();i++){ qualFileNames[i]->close(); delete qualFileNames[i]; }
+ //for(int i=0;i<qualFileNames.size();i++){ qualFileNames[i]->close(); delete qualFileNames[i]; }
}
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
int success = 1;
- Sequence currSeq(inFASTA); gobble(inFASTA);
+ Sequence currSeq(inFASTA); m->gobble(inFASTA);
QualityScores currQual;
if(qFileName != ""){
- currQual = QualityScores(qFile, currSeq.getNumBases()); gobble(qFile);
+ currQual = QualityScores(qFile, currSeq.getNumBases()); m->gobble(qFile);
}
string origSeq = currSeq.getUnaligned();
}
outGroups << currSeq.getName() << '\t' << thisGroup << endl;
if(allFiles){
- currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
+ ofstream outTemp;
+ m->openOutputFileAppend(fastaNames[indexToFastaFile], outTemp);
+ //currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
+ currSeq.printSequence(outTemp);
+ outTemp.close();
if(qFileName != ""){
- currQual.printQScores(*qualFileNames[indexToFastaFile]);
+ //currQual.printQScores(*qualFileNames[indexToFastaFile]);
+ ofstream outTemp2;
+ m->openOutputFileAppend(qualNames[indexToFastaFile], outTemp2);
+ currQual.printQScores(outTemp2);
+ outTemp2.close();
}
}
}
count++;
}
- unsigned long int pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= line->end)) { break; }
-
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ unsigned long int pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= line->end)) { break; }
+ #else
+ if (inFASTA.eof()) { break; }
+ #endif
+
//report progress
if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
if (oligoFile != "") { outGroups.close(); }
if(qFileName != "") { qFile.close(); scrapQual.close(); outQual.close(); }
- for(int i=0;i<fastaFileNames.size();i++){
- fastaFileNames[i]->close();
- delete fastaFileNames[i];
- }
+ //for(int i=0;i<fastaFileNames.size();i++){
+ // fastaFileNames[i]->close();
+ // delete fastaFileNames[i];
+ //}
- if(qFileName != ""){
- for(int i=0;i<qualFileNames.size();i++){
- qualFileNames[i]->close();
- delete qualFileNames[i];
- }
- }
+ //if(qFileName != ""){
+ //for(int i=0;i<qualFileNames.size();i++){
+ //qualFileNames[i]->close();
+ //delete qualFileNames[i];
+ //}
+ //}
return count;
}
try {
//set file positions for fasta file
- fastaFilePos = divideFile(filename, processors);
+ fastaFilePos = m->divideFile(filename, processors);
if (qfilename == "") { return processors; }
map<string, int> firstSeqNames;
for (int i = 0; i < (fastaFilePos.size()-1); i++) {
ifstream in;
- openInputFile(filename, in);
+ m->openInputFile(filename, in);
in.seekg(fastaFilePos[i]);
Sequence temp(in);
//seach for filePos of each first name in the qfile and save in qfileFilePos
ifstream inQual;
- openInputFile(qfilename, inQual);
-
+ m->openInputFile(qfilename, inQual);
+
string input;
while(!inQual.eof()){
- input = getline(inQual);
+ input = m->getline(inQual);
if (input.length() != 0) {
if(input[0] == '>'){ //this is a sequence name line
}
inQual.close();
+
if (firstSeqNames.size() != 0) {
for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
try {
ifstream inOligos;
- openInputFile(oligoFile, inOligos);
+ m->openInputFile(oligoFile, inOligos);
ofstream test;
groupVector.push_back(group);
if(allFiles){
- outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+ outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
if(qFileName != ""){
- outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
+ outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
}
if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
- filesToRemove.insert((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+ filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
if(qFileName != ""){
- filesToRemove.insert((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
+ filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
}
}else {
- outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+ outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
if(qFileName != ""){
- outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+ outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
}
}
}
groupVector.push_back(group);
if(allFiles){
- outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
- outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+ outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
if(qFileName != ""){
- outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
- outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
+ outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+ outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
}
}
}else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
}
- gobble(inOligos);
+ m->gobble(inOligos);
}
inOligos.close();
for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
if (groupVector[itPrime->second] != "") { //there is a group for this primer
- outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
- outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
+ outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
+ outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
if(qFileName != ""){
- outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
- outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
+ outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
+ outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
}
}
}
projects / mothur.git / blobdiff