fasta = validParameter.validFile(parameters, "fasta", false);
if (fasta == "not found") {
fasta = m->getFastaFile();
- if (fasta != "") { fastafileNames.push_back(fasta); m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ if (fasta != "") {
+ fastafileNames.push_back(fasta);
+ m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
+ string simpleName = m->getSimpleName(fasta);
+ filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+ }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else {
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- vector<unsigned long long> positions = savedPositions[s];
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
+ vector<unsigned long long> positions;
+ if (savedPositions.size() != 0) { positions = savedPositions[s]; }
+ else {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFile(fastafileNames[s], processors);
+#else
+ if(processors != 1){
+ int numFastaSeqs = 0;
+ positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
+ }
+#endif
+ }
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
for (int i = 0; i < (positions.size()-1); i++) {
count++;
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
int num = 0;
processIDS.clear();
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
#else
vector<unsigned long long> positions;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
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)]));
}else {
int numFastaSeqs = 0;
positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numFastaSeqs / processors;
count++;
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
int num = 0;
processIDS.clear();
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {