sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index e937b1661b90b5f8e3340178222c21a9a9cd8d9e..c9e5ecfdfda727427793e98aaed0270cdcd6e046 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -564,7 +564,7 @@ void PairwiseSeqsCommand::createProcesses(string filename) {
                        string extension = toString(i) + ".temp";
 
                        // Allocate memory for thread data.
-                       pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, i);
+                       pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, cutoff, i);
                        pDataArray.push_back(tempDist);
                        processIDS.push_back(i);
                        
@@ -643,8 +643,7 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
                outFile << setprecision(4);
                
                if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
-               int countSmall = 0;
-        int countAll = 0;
+               
                for(int i=startLine;i<endLine;i++){
                        if(output == "lt")      {       
                                string name = alignDB.get(i).getName();
@@ -682,9 +681,6 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
                 //cout << "dist = " << dist << endl;
                                                
                                if(dist <= cutoff){
-                    if (dist < 0.01) { countSmall++; }
-                    countAll++;
-
                                        if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
                                }
                                if (output == "lt") {  outFile << dist << '\t'; }
@@ -698,7 +694,7 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
                        
                }
                m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-               cout << "num less than 0.01 = " << countSmall << " of " << countAll << endl;
+               
                outFile.close();
         delete alignment;
         delete distCalculator;