chimera.slayer debugging

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 40855d0a262a49bf64488ec53f8f9b58b1beffea..438d90c30961dfbabe5436483f3d33a23fc537ae 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -14,15 +14,15 @@
 
 /**************************************************************************************************/
 
-BlastDB::BlastDB(float gO, float gE, float m, float mM) : Database(), 
+BlastDB::BlastDB(string tag, float gO, float gE, float m, float mM) : Database(), 
 gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
        
        count = 0;
 
        int randNumber = rand();
-       dbFileName = toString(randNumber) + ".template.unaligned.fasta";
-       queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
-       blastFileName = toString(randNumber) + ".blast";
+       dbFileName = tag + toString(randNumber) + ".template.unaligned.fasta";
+       queryFileName = tag + toString(randNumber) + ".candidate.unaligned.fasta";
+       blastFileName = tag + toString(randNumber) + ".blast";
 
 }
 /**************************************************************************************************/
@@ -128,6 +128,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                //      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 = 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());
@@ -147,7 +148,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                        //while (!m8FileHandle.eof())   {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }else{ cout << c; }     } //
                                //cout << endl;
                        m->gobble(m8FileHandle);
-                       if (searchScore >= minPerID) {
+                       if (searchScore >= minPerID) { 
                                topMatches.push_back(templateAccession);
                                Scores.push_back(searchScore);
                        }