working on search=dist in chimera.slayer

diff --git a/blastdb.cpp b/blastdb.cpp
index 2d171391ca24ff1bfa43146de6ac5385de6ed46f..d227bc6a88cc8553181065680c7dc56fd1707a21 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;
+//             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) {

diff --git a/slayer.cpp b/slayer.cpp
index 61b7b6341c6cfaaf7adf5158cfe5248c59507388..8e17f87b109500f34abb0aa573b263627011c19a 100644 (file)
--- a/slayer.cpp
+++ b/slayer.cpp
@@ -61,16 +61,16 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
                                                
                                                
                                                //are we within 10 points of the bootstrap cutoff?
-                                               if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
-                                                       bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
-                                                               
-                                                       if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
-                                                               
-                                                       divs[k].bsa = BS_A;
-                                                       divs[k].bsb = BS_B;
-                                                       divs[k].bsMax = max(BS_A, BS_B);
-                                                       divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
-                                               }
+//                                             if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
+//                                                     bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
+//                                                             
+//                                                     if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
+//                                                             
+//                                                     divs[k].bsa = BS_A;
+//                                                     divs[k].bsb = BS_B;
+//                                                     divs[k].bsMax = max(BS_A, BS_B);
+//                                                     divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
+//                                             }
                                                
                                                //so results reflect orignal alignment
                                                divs[k].winLStart = spots[divs[k].winLStart];