added namefile to align.check and added seqs from namefile to optimizing piece of...

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 407850f6ef80ac0c0d47811b785873d67f03e319..9a2851e343c2a151811770d32c1a71f75092c231 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -15,7 +15,7 @@
 //**********************************************************************************************************************
 vector<string> SeqErrorCommand::getValidParameters(){  
        try {
-               string Array[] =  {"query", "reference", "name", "qfile", "report", "threshold", "inputdir", "outputdir"};
+               string Array[] =  {"query", "reference", "name", "qfile", "report", "threshold", "ignorechimeras", "inputdir", "outputdir"};
                vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                return myArray;
        }
@@ -230,6 +230,8 @@ int SeqErrorCommand::execute(){
        try{
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
+               maxLength = 2000;
+               
                string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
                m->openOutputFile(errorSummaryFileName, errorSummaryFile);
                outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
@@ -259,11 +261,11 @@ int SeqErrorCommand::execute(){
                        m->openInputFile(qualFileName, qualFile);
                        report = ReportFile(reportFile, reportFileName);
                        
-                       qualForwardMap.resize(1000);
-                       qualReverseMap.resize(1000);
-                       for(int i=0;i<1000;i++){
-                               qualForwardMap[i].assign(100,0);
-                               qualReverseMap[i].assign(100,0);
+                       qualForwardMap.resize(maxLength);
+                       qualReverseMap.resize(maxLength);
+                       for(int i=0;i<maxLength;i++){
+                               qualForwardMap[i].assign(maxLength,0);
+                               qualReverseMap[i].assign(maxLength,0);
                        }                               
                }
                
@@ -282,18 +284,18 @@ int SeqErrorCommand::execute(){
                qScoreErrorMap['a'].assign(41, 0);
                
                map<char, vector<int> > errorForward;
-               errorForward['m'].assign(1000,0);
-               errorForward['s'].assign(1000,0);
-               errorForward['i'].assign(1000,0);
-               errorForward['d'].assign(1000,0);
-               errorForward['a'].assign(1000,0);
+               errorForward['m'].assign(maxLength,0);
+               errorForward['s'].assign(maxLength,0);
+               errorForward['i'].assign(maxLength,0);
+               errorForward['d'].assign(maxLength,0);
+               errorForward['a'].assign(maxLength,0);
                
                map<char, vector<int> > errorReverse;
-               errorReverse['m'].assign(1000,0);
-               errorReverse['s'].assign(1000,0);
-               errorReverse['i'].assign(1000,0);
-               errorReverse['d'].assign(1000,0);
-               errorReverse['a'].assign(1000,0);       
+               errorReverse['m'].assign(maxLength,0);
+               errorReverse['s'].assign(maxLength,0);
+               errorReverse['i'].assign(maxLength,0);
+               errorReverse['d'].assign(maxLength,0);
+               errorReverse['a'].assign(maxLength,0);  
                
 
                string errorChimeraFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.chimera";
@@ -716,7 +718,7 @@ void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map
                outputNames.push_back(errorForwardFileName);  outputTypes["error.forward"].push_back(errorForwardFileName);
 
                errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
-               for(int i=0;i<1000;i++){
+               for(int i=0;i<maxLength;i++){
                        float match = (float)errorForward['m'][i];
                        float subst = (float)errorForward['s'][i];
                        float insert = (float)errorForward['i'][i];
@@ -734,7 +736,7 @@ void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map
                outputNames.push_back(errorReverseFileName);  outputTypes["error.reverse"].push_back(errorReverseFileName);
 
                errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
-               for(int i=0;i<1000;i++){
+               for(int i=0;i<maxLength;i++){
                        float match = (float)errorReverse['m'][i];
                        float subst = (float)errorReverse['s'][i];
                        float insert = (float)errorReverse['i'][i];