initialized numLinkers and numSpacers in trim.seqs and trim.flows

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 9ac7c5bcef6fee9c8e01b7838a3560f3478c5fcc..9bda05a912551eca035bdd776387954619f5a8d8 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -176,7 +176,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
-                       else if (queryFileName == "not open") { abort = true; } 
+                       else if (queryFileName == "not open") { queryFileName = ""; abort = true; }     
                        else { m->setFastaFile(queryFileName); }
                        
                        referenceFileName = validParameter.validFile(parameters, "reference", true);
@@ -246,6 +246,11 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 
                        substitutionMatrix.resize(6);
                        for(int i=0;i<6;i++){   substitutionMatrix[i].resize(6,0);      }
+                       
+                       if ((namesFileName == "") && (queryFileName != "")){
+                               vector<string> files; files.push_back(queryFileName); 
+                               parser.getNameFile(files);
+                       }
                }
        }
        catch(exception& e) {
@@ -293,7 +298,7 @@ int SeqErrorCommand::execute(){
                if(qualFileName == "")  {       qLines = lines; rLines = lines; } //fills with duds
                
                int numSeqs = 0;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                if(processors == 1){
                        numSeqs = driver(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName, lines[0], qLines[0], rLines[0]);
                }else{
@@ -361,7 +366,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
                processIDS.clear();
                map<char, vector<int> >::iterator it;
                int num = 0;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                
                //loop through and create all the processes you want
                while (process != processors) {
@@ -734,7 +739,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                        
                        index++;
                        
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                unsigned long long pos = queryFile.tellg();
                                if ((pos == -1) || (pos >= line.end)) { break; }
                        #else
@@ -1210,7 +1215,7 @@ void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector
 
 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)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                //set file positions for fasta file
                fastaFilePos = m->divideFile(filename, processors);