working on chimera.perseus. made removeConfidences function smarter. Fixed bug in...

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index fc027b9261822880ac0afa1cc99929791a309df4..253e03e2a1d380cb4d13f360fc9a5fecaaeb0808 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -178,7 +178,11 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        }
                        else if (queryFileName == "not open") { abort = true; } 
                        else { m->setFastaFile(queryFileName); }
-
+                       
+                       referenceFileName = validParameter.validFile(parameters, "reference", true);
+                       if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
+                       else if (referenceFileName == "not open") { abort = true; }     
+                       
                        //check for optional parameters
                        namesFileName = validParameter.validFile(parameters, "name", true);
                        if(namesFileName == "not found"){       namesFileName = "";     }
@@ -273,9 +277,9 @@ int SeqErrorCommand::execute(){
 
                if(namesFileName != ""){        weights = getWeights(); }
                
-               vector<unsigned long int> fastaFilePos;
-               vector<unsigned long int> qFilePos;
-               vector<unsigned long int> reportFilePos;
+               vector<unsigned long long> fastaFilePos;
+               vector<unsigned long long> qFilePos;
+               vector<unsigned long long> reportFilePos;
                
                setLines(queryFileName, qualFileName, reportFileName, fastaFilePos, qFilePos, reportFilePos);
                
@@ -306,7 +310,7 @@ int SeqErrorCommand::execute(){
                
                printErrorFRFile(errorForward, errorReverse);
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 
                string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.count";
                ofstream errorCountFile;
@@ -321,7 +325,7 @@ int SeqErrorCommand::execute(){
                }
                errorCountFile.close();
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 
                printSubMatrix();
                                
@@ -478,11 +482,11 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
                        m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
                        
                        m->appendFiles((summaryFileName + toString(processIDS[i]) + ".temp"), summaryFileName);
-                       remove((summaryFileName + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((summaryFileName + toString(processIDS[i]) + ".temp"));
                        m->appendFiles((errorOutputFileName + toString(processIDS[i]) + ".temp"), errorOutputFileName);
-                       remove((errorOutputFileName + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((errorOutputFileName + toString(processIDS[i]) + ".temp"));
                        m->appendFiles((chimeraOutputFileName + toString(processIDS[i]) + ".temp"), chimeraOutputFileName);
-                       remove((chimeraOutputFileName + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((chimeraOutputFileName + toString(processIDS[i]) + ".temp"));
                        
                        ifstream in;
                        string tempFile =  filename + toString(processIDS[i]) + ".info.temp";
@@ -577,7 +581,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
                        }
                        m->gobble(in);
                        
-                       in.close(); remove(tempFile.c_str());
+                       in.close(); m->mothurRemove(tempFile);
                        
                }
 #endif         
@@ -731,7 +735,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                        index++;
                        
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               unsigned long int pos = queryFile.tellg();
+                               unsigned long long pos = queryFile.tellg();
                                if ((pos == -1) || (pos >= line.end)) { break; }
                        #else
                                if (queryFile.eof()) { break; }
@@ -1204,7 +1208,7 @@ void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector
 }
 /**************************************************************************************************/
 
-int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos, vector<unsigned long int>& rfileFilePos) {
+int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector<unsigned long long>& fastaFilePos, vector<unsigned long long>& qfileFilePos, vector<unsigned long long>& rfileFilePos) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                //set file positions for fasta file
@@ -1246,7 +1250,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                                        map<string, int>::iterator it = firstSeqNames.find(sname);
                                        
                                        if(it != firstSeqNames.end()) { //this is the start of a new chunk
-                                               unsigned long int pos = inQual.tellg(); 
+                                               unsigned long long pos = inQual.tellg(); 
                                                qfileFilePos.push_back(pos - input.length() - 1);       
                                                firstSeqNames.erase(it);
                                        }
@@ -1267,7 +1271,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                
                //get last file position of qfile
                FILE * pFile;
-               unsigned long int size;
+               unsigned long long size;
                
                //get num bytes in file
                pFile = fopen (qfilename.c_str(),"rb");
@@ -1305,7 +1309,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                                map<string, int>::iterator it = firstSeqNamesReport.find(sname);
                        
                                if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk
-                                       unsigned long int pos = inR.tellg(); 
+                                       unsigned long long pos = inR.tellg(); 
                                        rfileFilePos.push_back(pos - input.length() - 1);       
                                        firstSeqNamesReport.erase(it);
                                }
@@ -1326,7 +1330,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                
                //get last file position of qfile
                FILE * rFile;
-               unsigned long int sizeR;
+               unsigned long long sizeR;
                
                //get num bytes in file
                rFile = fopen (rfilename.c_str(),"rb");
@@ -1346,7 +1350,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                fastaFilePos.push_back(0); qfileFilePos.push_back(0);
                //get last file position of fastafile
                FILE * pFile;
-               unsigned long int size;
+               unsigned long long size;
                
                //get num bytes in file
                pFile = fopen (filename.c_str(),"rb");