//**********************************************************************************************************************
TrimSeqsCommand::TrimSeqsCommand(){
try {
+ abort = true;
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
}
ofstream outGroups;
- vector<ofstream*> fastaFileNames;
- vector<ofstream*> qualFileNames;
+ //vector<ofstream*> fastaFileNames;
+ //vector<ofstream*> qualFileNames;
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));
+ 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
}
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()); }
}
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();
}
}
}
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;
}
//seach for filePos of each first name in the qfile and save in qfileFilePos
ifstream inQual;
m->openInputFile(qfilename, inQual);
-
+
string input;
while(!inQual.eof()){
input = m->getline(inQual);
}
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();