X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=myPerseus.cpp;h=f7cb65ec43c741a1d4ae5be194fd49fa75b2fc9e;hp=b342393aa9a82e3dcb00190f6648edc7110779b3;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=74dc92cf53df65fd8b14d8eaf35489bbecbccac6

diff --git a/myPerseus.cpp b/myPerseus.cpp
index b342393..f7cb65e 100644
--- 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;					
 						}