captured stdout from system command, fixed bug in trim.seqs added error checks for...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index dc87fff99489ebe9ebfc29bec6ff2328875d7030..4d6b45da96664677f61908874d79b8d847f0e74c 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -555,7 +555,6 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        int currentSeqsDiffs = 0;
 
                        Sequence currSeq(inFASTA); m->gobble(inFASTA);
-                       
                        QualityScores currQual;
                        if(qFileName != ""){
                                currQual = QualityScores(qFile);  m->gobble(qFile);
@@ -711,17 +710,18 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                unsigned long int pos = inFASTA.tellg();
                                if ((pos == -1) || (pos >= line->end)) { break; }
+                       
                        #else
                                if (inFASTA.eof()) { break; }
                        #endif
-                               
+                       
                        //report progress
                        if((count) % 1000 == 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
                        
                }
                //report progress
                if((count) % 1000 != 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
-
+               
                
                inFASTA.close();
                trimFASTAFile.close();
@@ -798,14 +798,18 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                                                 qLines[process]);
                                
                                //pass groupCounts to parent
-                               ofstream out;
-                               string tempFile = filename + toString(getpid()) + ".num.temp";
-                               m->openOutputFile(tempFile, out);
-                               for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
-                                       out << it->first << '\t' << it->second << endl;
+                               if(oligoFile != ""){
+                                       ofstream out;
+                                       string tempFile = filename + toString(getpid()) + ".num.temp";
+                                       m->openOutputFile(tempFile, out);
+                                       
+                                       out << groupCounts.size() << endl;
+                                       
+                                       for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+                                               out << it->first << '\t' << it->second << endl;
+                                       }
+                                       out.close();
                                }
-                               out.close();
-                               
                                exit(0);
                        }else { 
                                m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
@@ -859,8 +863,10 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                remove((scrapNameFileName + toString(processIDS[i]) + ".temp").c_str());
                        }
                        
-                       m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
-                       remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
+                       if(oligoFile != ""){
+                               m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
+                               remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
+                       }
                        
                        
                        if(allFiles){
@@ -884,19 +890,26 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                }
                        }
                        
-                       ifstream in;
-                       string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
-                       m->openInputFile(tempFile, in);
-                       int tempNum;
-                       string group;
-                       while (!in.eof()) { 
-                               in >> group >> tempNum; m->gobble(in);
+                       if(oligoFile != ""){
+                               ifstream in;
+                               string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
+                               m->openInputFile(tempFile, in);
+                               int tempNum;
+                               string group;
                                
-                               map<string, int>::iterator it = groupCounts.find(group);
-                               if (it == groupCounts.end()) {  groupCounts[group] = tempNum; }
-                               else { groupCounts[it->first] += tempNum; }
+                               in >> tempNum; m->gobble(in);
+                               
+                               if (tempNum != 0) {
+                                       while (!in.eof()) { 
+                                               in >> group >> tempNum; m->gobble(in);
+                               
+                                               map<string, int>::iterator it = groupCounts.find(group);
+                                               if (it == groupCounts.end()) {  groupCounts[group] = tempNum; }
+                                               else { groupCounts[it->first] += tempNum; }
+                                       }
+                               }
+                               in.close(); remove(tempFile.c_str());
                        }
-                       in.close(); remove(tempFile.c_str());
                        
                }