working on search=dist in chimera.slayer

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 438d90c30961dfbabe5436483f3d33a23fc537ae..2d171391ca24ff1bfa43146de6ac5385de6ed46f 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -123,7 +123,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
                queryFile.close();
-                               
+               cout << seq->getUnaligned() << endl;
                //      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.
@@ -142,7 +142,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                
                while(!m8FileHandle.eof()){
                        m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
-                       //cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl; 
+                       cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl; 
                        
                        //get rest of junk in line
                        //while (!m8FileHandle.eof())   {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }else{ cout << c; }     } //
@@ -157,7 +157,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                m8FileHandle.close();
                remove((queryFileName+seq->getName()).c_str());
                remove((blastFileName+seq->getName()).c_str());
-//cout << "\n" ;               
+cout << "\n" ;         
                return topMatches;
        }
        catch(exception& e) {