X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=c9e5ecfdfda727427793e98aaed0270cdcd6e046;hp=767fdb52702bd1a3652d6bf2c1e2b244958e48ca;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 767fdb5..c9e5ecf 100644
--- 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);
 			
@@ -672,10 +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; }
 				}