}
}
else if(method == "suffix") { database = new SuffixDB(numSeqs); }
- else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, ""); }
+ else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID); }
else if(method == "distance") { database = new DistanceDB(); }
else {
m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
names.push_back(temp.getName());
database->addSequence(temp);
}
- database->generateDB();
+// database->generateDB();
}else if ((method == "kmer") && (!needToGenerate)) {
ifstream kmerFileTest(kmerDBName.c_str());
database->readKmerDB(kmerFileTest);
m->mothurOut("Generating search database... "); cout.flush();
#ifdef USE_MPI
int pid, processors;
- vector<unsigned long int> positions;
+ vector<unsigned long long> positions;
int tag = 2001;
MPI_Status status;
//create database
if(method == "kmer") { database = new KmerDB(tempFile, kmerSize); }
else if(method == "suffix") { database = new SuffixDB(numSeqs); }
- else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch); }
+ else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", pid); }
else if(method == "distance") { database = new DistanceDB(); }
else {
m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8."); m->mothurOutEndLine();
}
}
- database->generateDB();
+// database->generateDB();
MPI_File_close(&inMPI);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
}
}
else if(method == "suffix") { database = new SuffixDB(numSeqs); }
- else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, ""); }
+ else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID); }
else if(method == "distance") { database = new DistanceDB(); }
else {
m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
}
fastaFile.close();
- database->generateDB();
+// database->generateDB();
}else if ((method == "kmer") && (!needToGenerate)) {
ifstream kmerFileTest(kmerDBName.c_str());
database->setNumSeqs(names.size());
//sanity check
- bool okay = phyloTree->ErrorCheck(names);
+ //bool okay = phyloTree->ErrorCheck(names);
- if (!okay) { m->control_pressed = true; }
+ //if (!okay) { m->control_pressed = true; }
m->mothurOut("DONE."); m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
#ifdef USE_MPI
int pid, num, processors;
- vector<unsigned long int> positions;
+ vector<unsigned long long> positions;
int tag = 2001;
MPI_Status status;