//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
}else{
string simpleName = m->getSimpleName(fastafileNames[i]);
filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+ m->setFastaFile(fastafileNames[i]);
}
in.close();
}
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
vertical = validParameter.validFile(parameters, "vertical", false);
if (vertical == "not found") {
if(filter[i] == '1'){ filteredLength++; }
}
- if (m->control_pressed) { outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
#ifdef USE_MPI
int pid, numSeqsPerProcessor, num;
int tag = 2001;
- vector<unsigned long int>MPIPos;
+ vector<unsigned long long>MPIPos;
MPI_Status status;
MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
-
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
+
for (int i = 0; i < (positions.size()-1); i++) {
lines.push_back(new linePair(positions[i], positions[(i+1)]));
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
if(processors == 1){
int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
//append fasta files
for(int i=1;i<processors;i++){
m->appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
- remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((fastafileNames[s] + toString(processIDS[i]) + ".temp"));
}
}
if (m->control_pressed) { return 1; }
#else
+ lines.push_back(new linePair(0, 1000));
int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
}
#ifdef USE_MPI
/**************************************************************************************/
-int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
+int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {
try {
string outputString = "";
int count = 0;
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- unsigned long int pos = in.tellg();
+ unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
if (in.eof()) { break; }
string tempFile = filename + toString(processIDS[i]) + ".num.temp";
m->openInputFile(tempFile, in);
if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
- in.close(); remove(tempFile.c_str());
+ in.close(); m->mothurRemove(tempFile);
}
#ifdef USE_MPI
int pid, numSeqsPerProcessor, num;
int tag = 2001;
- vector<unsigned long int> MPIPos;
+ vector<unsigned long long> MPIPos;
MPI_Status status;
MPI_File inMPI;
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
- for (int i = 0; i < (positions.size()-1); i++) {
- lines.push_back(new linePair(positions[i], positions[(i+1)]));
- }
+
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
+ for (int i = 0; i < (positions.size()-1); i++) {
+ lines.push_back(new linePair(positions[i], positions[(i+1)]));
+ }
+
if(processors == 1){
int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
if (m->control_pressed) { return filterString; }
#else
+ lines.push_back(new linePair(0, 1000));
int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
if (m->control_pressed) { return filterString; }
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- unsigned long int pos = in.tellg();
+ unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
if (in.eof()) { break; }
}
#ifdef USE_MPI
/**************************************************************************************/
-int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {
+int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long long>& MPIPos) {
try {
MPI_Status status;
for (int k = 0; k < alignmentLength; k++) { in >> temp; F.gap[k] += temp; } m->gobble(in);
in.close();
- remove(tempFilename.c_str());
+ m->mothurRemove(tempFilename);
}
return num;