sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 0f8602871561c20804b49bdc948da6194b25adbe..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);
                        
@@ -581,6 +581,9 @@ void PairwiseSeqsCommand::createProcesses(string filename) {
                
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
+            if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
                        CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }
@@ -669,10 +672,14 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
                                seqI.setAligned(alignment->getSeqAAln());
                                seqJ.setAligned(alignment->getSeqBAln());
 
-                               
+                               //cout << seqI.getName() << '\t' << seqJ.getName() << endl;
+                //cout << alignment->getSeqAAln() << endl << alignment->getSeqBAln() << endl;
+                
                                distCalculator->calcDist(seqI, seqJ);
                                double dist = distCalculator->getDist();
-                               
+                
+                //cout << "dist = " << dist << endl;
+                                               
                                if(dist <= cutoff){
                                        if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
                                }