random chagnes from pat

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 9a2851e343c2a151811770d32c1a71f75092c231..5a0cc02fab59de9960e6626b4cbcc87e8ce82d1f 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -264,8 +264,8 @@ int SeqErrorCommand::execute(){
                        qualForwardMap.resize(maxLength);
                        qualReverseMap.resize(maxLength);
                        for(int i=0;i<maxLength;i++){
-                               qualForwardMap[i].assign(maxLength,0);
-                               qualReverseMap[i].assign(maxLength,0);
+                               qualForwardMap[i].assign(41,0);
+                               qualReverseMap[i].assign(41,0);
                        }                               
                }
                
@@ -780,17 +780,15 @@ void SeqErrorCommand::printErrorQuality(map<char, vector<int> > qScoreErrorMap){
 //***************************************************************************************************************
 
 void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector<vector<int> > qualReverseMap){
-       try{
-
 
-               int lastRow = 0;
-               int lastColumn = 0;
+       try{
+               int numRows = 0;
+               int numColumns = qualForwardMap[0].size();
 
                for(int i=0;i<qualForwardMap.size();i++){
-                       for(int j=0;j<qualForwardMap[i].size();j++){
+                       for(int j=0;j<numColumns;j++){
                                if(qualForwardMap[i][j] != 0){
-                                       if(lastRow < i)         {       lastRow = i+2;          }
-                                       if(lastColumn < j)      {       lastColumn = j+2;       }
+                                       if(numRows < i)         {       numRows = i+20;         }
                                }
                        }
                }
@@ -800,11 +798,11 @@ void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector
                m->openOutputFile(qualityForwardFileName, qualityForwardFile);
                outputNames.push_back(qualityForwardFileName);  outputTypes["error.qual.forward"].push_back(qualityForwardFileName);
 
-               for(int i=0;i<lastColumn;i++){  qualityForwardFile << '\t' << i;        }       qualityForwardFile << endl;
+               for(int i=0;i<numColumns;i++){  qualityForwardFile << '\t' << i;        }       qualityForwardFile << endl;
 
-               for(int i=0;i<lastRow;i++){
+               for(int i=0;i<numRows;i++){
                        qualityForwardFile << i+1;
-                       for(int j=0;j<lastColumn;j++){
+                       for(int j=0;j<numColumns;j++){
                                qualityForwardFile << '\t' << qualForwardMap[i][j];
                        }
 
@@ -818,11 +816,11 @@ void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector
                m->openOutputFile(qualityReverseFileName, qualityReverseFile);
                outputNames.push_back(qualityReverseFileName);  outputTypes["error.qual.reverse"].push_back(qualityReverseFileName);
                
-               for(int i=0;i<lastColumn;i++){  qualityReverseFile << '\t' << i;        }       qualityReverseFile << endl;
-               for(int i=0;i<lastRow;i++){
+               for(int i=0;i<numColumns;i++){  qualityReverseFile << '\t' << i;        }       qualityReverseFile << endl;
+               for(int i=0;i<numRows;i++){
                        
                        qualityReverseFile << i+1;
-                       for(int j=0;j<lastColumn;j++){
+                       for(int j=0;j<numColumns;j++){
                                qualityReverseFile << '\t' << qualReverseMap[i][j];
                        }
                        qualityReverseFile << endl;
@@ -833,7 +831,7 @@ void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector
                m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
                exit(1);
        }
+       
 }
 
-
 //***************************************************************************************************************