Fixed a bug in the count output of seq.error when using multiple processors

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 67e43aa0d4b7f6a6ff251bc45a8254ca49b8b162..99e789399e90c2b2adc429330177e7bd579e8354 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -407,6 +407,13 @@ int SeqErrorCommand::execute(){
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");
                m->mothurOutEndLine();
                
+        //set fasta file as new current fastafile
+               string current = "";
+               itTypes = outputTypes.find("errorseq");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+               }
+        
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
@@ -636,7 +643,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
                        int misMatchSize;
                        in >> misMatchSize; m->gobble(in);
                        if (misMatchSize > misMatchCounts.size()) {     misMatchCounts.resize(misMatchSize, 0); }
-                       for (int j = 0; j < misMatchCounts.size(); j++) {
+                       for (int j = 0; j < misMatchSize; j++) {
                                in >> tempNum; misMatchCounts[j] += tempNum;
                        }
                        m->gobble(in);
@@ -673,10 +680,10 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                int numSeqs = 0;
                
                map<string, int>::iterator it;
-               qScoreErrorMap['m'].assign(41, 0);
-               qScoreErrorMap['s'].assign(41, 0);
-               qScoreErrorMap['i'].assign(41, 0);
-               qScoreErrorMap['a'].assign(41, 0);
+               qScoreErrorMap['m'].assign(101, 0);
+               qScoreErrorMap['s'].assign(101, 0);
+               qScoreErrorMap['i'].assign(101, 0);
+               qScoreErrorMap['a'].assign(101, 0);
                
                errorForward['m'].assign(maxLength,0);
                errorForward['s'].assign(maxLength,0);
@@ -712,8 +719,8 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                        qualForwardMap.resize(maxLength);
                        qualReverseMap.resize(maxLength);
                        for(int i=0;i<maxLength;i++){
-                               qualForwardMap[i].assign(41,0);
-                               qualReverseMap[i].assign(41,0);
+                               qualForwardMap[i].assign(101,0);
+                               qualReverseMap[i].assign(101,0);
                        }       
                }
                else if(qFileName != "" && !aligned){
@@ -724,8 +731,8 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                        qualForwardMap.resize(maxLength);
                        qualReverseMap.resize(maxLength);
                        for(int i=0;i<maxLength;i++){
-                               qualForwardMap[i].assign(41,0);
-                               qualReverseMap[i].assign(41,0);
+                               qualForwardMap[i].assign(101,0);
+                               qualReverseMap[i].assign(101,0);
                        }       
         }
         
@@ -1271,7 +1278,7 @@ void SeqErrorCommand::printErrorQuality(map<char, vector<int> > qScoreErrorMap){
                outputNames.push_back(errorQualityFileName);  outputTypes["errorquality"].push_back(errorQualityFileName);
 
                errorQualityFile << "qscore\tmatches\tsubstitutions\tinsertions\tambiguous" << endl;
-               for(int i=0;i<41;i++){
+               for(int i=0;i<101;i++){
                        errorQualityFile << i << '\t' << qScoreErrorMap['m'][i] << '\t' << qScoreErrorMap['s'][i] << '\t' << qScoreErrorMap['i'][i] << '\t'<< qScoreErrorMap['a'][i] << endl;
                }
                errorQualityFile.close();
@@ -1381,6 +1388,10 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                                        
                                        string sname = "";  nameStream >> sname;
                                        sname = sname.substr(1);
+                    
+                    for (int i = 0; i < sname.length(); i++) {
+                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+                    }
                                        
                                        map<string, int>::iterator it = firstSeqNames.find(sname);
                                        
@@ -1441,6 +1452,10 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                     istringstream nameStream(input);
                     string sname = "";  nameStream >> sname;
                     
+                    for (int i = 0; i < sname.length(); i++) {
+                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+                    }
+                    
                     map<string, int>::iterator it = firstSeqNamesReport.find(sname);
                 
                     if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk