if (flowFileVector.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
}
else{
- outputDir += m->hasPath(flowFileName);
+ if (outputDir == "") { outputDir = m->hasPath(flowFileName); }
flowFileVector.push_back(flowFileName);
}
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(filename); }
+ if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.qual";
ofstream qualityFile;
void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTUs, int numFlowCells, string filename, vector<int> otuCounts, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& centroids){
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(filename); }
+ if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.fasta";
ofstream fastaFile;
m->openOutputFile(fastaFileName, fastaFile);
void ShhherCommand::writeNames(string thisCompositeNamesFileName, int numOTUs, string filename, vector<int> otuCounts, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU){
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(filename); }
+ if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.names";
ofstream nameFile;
m->openOutputFile(nameFileName, nameFile);
void ShhherCommand::writeGroups(string filename, int numSeqs, vector<string>& seqNameVector){
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(filename); }
+ if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(filename));
string groupFileName = fileRoot + "shhh.groups";
ofstream groupFile;
void ShhherCommand::writeClusters(string filename, int numOTUs, int numFlowCells, vector<int> otuCounts, vector<int>& centroids, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU, vector<int>& lengths, vector<short>& flowDataIntI){
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(filename); }
+ if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.counts";
ofstream otuCountsFile;
m->openOutputFile(otuCountsFileName, otuCountsFile);