changes for chimera slayer

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index fdb5456050bcce78b620e9d3d697a334626a54ae..3e1210b46abaa4c01314a8702feea3eded345c11 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -111,9 +111,10 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 }
 /**************************************************************************************************/
 //assumes you have added all the template sequences using the addSequence function and run generateDB.
-vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
+vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
        try{
                vector<int> topMatches;
+               float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score;
                Scores.clear();
                
                ofstream queryFile;
@@ -126,7 +127,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                //      the goal here is to quickly survey the database to find the closest match.  To do this we are using the default
                //      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());
@@ -134,20 +135,22 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                ifstream m8FileHandle;
                m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
        
-               string dummy;
+               string dummy, eScore;
                int templateAccession;
                m->gobble(m8FileHandle);
                
                while(!m8FileHandle.eof()){
-                       m8FileHandle >> dummy >> templateAccession >> searchScore;
-                       //cout << templateAccession << '\t' << searchScore << endl;
+                       m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
+                       //cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t';
                        
                        //get rest of junk in line
-                       while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       } 
-                       
+                       //while (!m8FileHandle.eof())   {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }else{ cout << c; }     } //
+                               //cout << endl;
                        m->gobble(m8FileHandle);
-                       topMatches.push_back(templateAccession);
-                       Scores.push_back(searchScore);
+                       if (score >= minPerID) {
+                               topMatches.push_back(templateAccession);
+                               Scores.push_back(searchScore);
+                       }
 //cout << templateAccession << endl;
                }
                m8FileHandle.close();