created blank accnos in chimera commands if no seqs are deemed chimeric. modified...

[mothur.git] / readblast.cpp

diff --git a/readblast.cpp b/readblast.cpp
index 4833d0125d8a286e0116be5ae0644c33f5443803..c3dfd4884f0d01d6c9dbb98c17aa9a8341a44c5d 100644 (file)
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -177,8 +177,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                                
                                                //if we have it then compare
                                                if (itDist != dists[it->first].end()) {
-               if (distance < 0.0) { cout << currentRow << '\t' << nameMap->get(it->first) << '\t' << "score = " << it->second << " refscore = " << refScore << " distance = " << distance << " distance = " << itDist->second << endl;        }
-
+       
                                                        //if you want the minimum blast score ratio, then pick max distance
                                                        if(minWanted) {  distance = max(itDist->second, distance);  }
                                                        else{   distance = min(itDist->second, distance);  }
@@ -314,8 +313,8 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
                ifstream in;
                openInputFile(blastfile, in);
                
-               ofstream outName;
-               openOutputFile("tempOutNames", outName);
+               //ofstream outName;
+               //openOutputFile((blastfile + ".tempOutNames"), outName);
                
                //read first line
                in >> prevName;
@@ -351,6 +350,7 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
                //openOutputFile(outNames, out);
                //nameMap->print(out);
                //out.close();
+               
                if (m->control_pressed) { return 0; }
                
                m->mothurOut(toString(num) + " names read."); m->mothurOutEndLine();