added parameter to chimera.uchime

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 70349e50f0264b68fba76c4f04ebbddd0c8c96f6..b1a7b48d1108d747c1423eb0f8bad19e3ceede42 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -83,8 +83,10 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                        blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
                        blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
                #else
-                       blastCommand =  "\"" + path + "blast\\bin\\blastall\" -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
+                       blastCommand =  "\"" + path + "blast\\bin\\blastall\" -p blastn -d " + "\"" + dbFileName + "\"" + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
                        blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
+                       //wrap entire string in ""
+                       blastCommand = "\"" + blastCommand + "\"";
                #endif
                system(blastCommand.c_str());
                
@@ -140,8 +142,11 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                        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 =  "\"" + 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());
+                       //wrap entire string in ""
+                       blastCommand = "\"" + blastCommand + "\"";
+
                #endif
                
                system(blastCommand.c_str());
@@ -213,7 +218,9 @@ void BlastDB::generateDB() {
                #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;
+                       formatdbCommand = "\"" + path + "blast\\bin\\formatdb\" -p F -o T -i " + "\"" +  dbFileName + "\"";
+                       //wrap entire string in ""
+                       formatdbCommand = "\"" + formatdbCommand + "\"";
                #endif
                system(formatdbCommand.c_str());                                                                //      to get the right sequence names, i think. -p F
                                                                                                                                        //      option tells formatdb that seqs are DNA, not prot