added modify names parameter to set.dir

[mothur.git] / myPerseus.cpp

diff --git a/myPerseus.cpp b/myPerseus.cpp
index b342393aa9a82e3dcb00190f6648edc7110779b3..f7cb65ec43c741a1d4ae5be194fd49fa75b2fc9e 100644 (file)
--- a/myPerseus.cpp
+++ b/myPerseus.cpp
@@ -515,7 +515,7 @@ int Perseus::getChimera(vector<seqData> sequences,
                        for(int i=0;i<numRefSeqs;i++){
                                
                                if(restricted[i] == 0){
-                                       if(leftDiffs[i][l] < singleLeft[l] && sequences[i].frequency || (leftDiffs[i][l] == singleLeft[l] && sequences[i].frequency > sequences[bestLeft[l]].frequency)){
+                                       if(((leftDiffs[i][l] < singleLeft[l]) && sequences[i].frequency) || ((leftDiffs[i][l] == singleLeft[l]) && (sequences[i].frequency > sequences[bestLeft[l]].frequency))){
                                                singleLeft[l] = leftDiffs[i][l];
                                                bestLeft[l] = i;
                                        }
@@ -533,7 +533,7 @@ int Perseus::getChimera(vector<seqData> sequences,
                        for(int i=0;i<numRefSeqs;i++){
                                
                                if(restricted[i] == 0){
-                                       if(rightDiffs[i][l] < singleRight[l] && sequences[i].frequency || (rightDiffs[i][l] == singleRight[l] && sequences[i].frequency > sequences[bestRight[l]].frequency)){
+                                       if((rightDiffs[i][l] < singleRight[l] && sequences[i].frequency) || ((rightDiffs[i][l] == singleRight[l] && sequences[i].frequency > sequences[bestRight[l]].frequency))){
                                                singleRight[l] = rightDiffs[i][l];
                                                bestRight[l] = i;
                                        }
@@ -548,7 +548,7 @@ int Perseus::getChimera(vector<seqData> sequences,
                rightParent = -1;
                breakPoint = -1;
                
-               for(int l=0;l<seqLength;l++){
+               for(int l=0;l<seqLength-1;l++){
                        
                        if (m->control_pressed) { return 0; }
                        
@@ -649,7 +649,7 @@ int Perseus::getTrimera(vector<seqData>& sequences,
                                        if(restricted[i] == 0){
                                                int delta = leftDiffs[i][y] - leftDiffs[i][x];
 
-                                               if(delta < minDelta[x][y] || delta == minDelta[x][y] && sequences[i].frequency > sequences[minDeltaSeq[x][y]].frequency){
+                                               if(delta < minDelta[x][y] || (delta == minDelta[x][y] && sequences[i].frequency > sequences[minDeltaSeq[x][y]].frequency)){
                                                        minDelta[x][y] = delta;
                                                        minDeltaSeq[x][y] = i;                                  
                                                }