string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
outputNames.push_back(scrapSeqFile);
string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
- outputNames.push_back(trimQualFile);
string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
- outputNames.push_back(scrapQualFile);
+ if (qFileName != "") { outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile); }
string groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
vector<string> fastaFileNames;
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());
vector<ofstream*> fastaFileNames;
vector<ofstream*> qualFileNames;
- cout << "here" << endl;
if (oligoFile != "") {
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));
if(qFileName != ""){
#endif
}
}
-cout << "here " << filename << endl;
+
ifstream inFASTA;
m->openInputFile(filename, inFASTA);
inFASTA.seekg(line->start);
- cout << "here " << qFileName << endl;
+
ifstream qFile;
if(qFileName != "") { m->openInputFile(qFileName, qFile); qFile.seekg(qline->start); }
bool done = false;
int count = 0;
- cout << "here" << endl;
+
while (!done) {
if (m->control_pressed) {