// wordsize used in megablast. I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
// long. With this setting, it seems comparable in speed to the suffix tree approach.
//7000004128189528left 0 100 66 0 0 1 66 61 126 1e-31 131
+ string blastCommand;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
+ #else
+ blastCommand = path + "blast\\bin\\megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
+ #endif
- string blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
- blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
system(blastCommand.c_str());
ifstream m8FileHandle;
for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
path = path.substr(0, (tempPath.find_last_of('m')));
- string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+ string formatdbCommand;
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+ #else
+ formatdbCommand = path + "blast\\bin\\formatdb -p F -o T -i " + dbFileName;
+ #endif
system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
// option tells formatdb that seqs are DNA, not prot
//m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); cout.flush();