fixed bug with trim.seqs allfiles=t

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index b4259bfddfa565d1a6982e6583009c3690c90089..2bb0e57566e59b39a04ce4b4968086894bf64355 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -78,6 +78,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        string temp;
@@ -313,10 +314,10 @@ int SeqErrorCommand::execute(){
                        else{   minCompare.weight = 1;  }
 
                        printErrorData(minCompare, numParentSeqs);
-
+               
                        if(!ignoreSeq){
-                               
-                               for(int i=0;i<minCompare.total;i++){
+
+                               for(int i=0;i<minCompare.sequence.length();i++){
                                        char letter = minCompare.sequence[i];
 
                                        errorForward[letter][i] += minCompare.weight;
@@ -429,12 +430,13 @@ void SeqErrorCommand::getReferences(){
                        int numAmbigs = currentSeq.getAmbigBases();
                        if(numAmbigs > 0){      numAmbigSeqs++; }
                        
-                       int startPos = currentSeq.getStartPos();
-                       if(startPos > maxStartPos)      {       maxStartPos = startPos; }
-
-                       int endPos = currentSeq.getEndPos();
-                       if(endPos < minEndPos)          {       minEndPos = endPos;             }
+//                     int startPos = currentSeq.getStartPos();
+//                     if(startPos > maxStartPos)      {       maxStartPos = startPos; }
+//
+//                     int endPos = currentSeq.getEndPos();
+//                     if(endPos < minEndPos)          {       minEndPos = endPos;             }
                        referenceSeqs.push_back(currentSeq);
+                               
                        m->gobble(referenceFile);
                }
                referenceFile.close();