changed sffinfo flow default to true. fixed bug in trim.seqs and filter.seqs related...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index f55272e5b08a0b6e84a3052be2eabbcc22b170f3..9913727dcdc8257816e1f83fab2f8a4b903ff1cd 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -371,7 +371,7 @@ int TrimSeqsCommand::execute(){
                                outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
                        }
                }
-               
+       
         //fills lines and qlines
                setLines(fastaFile, qFileName);
                
@@ -1071,8 +1071,6 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
                //set file positions for fasta file
                fastaFilePos = m->divideFile(filename, processors);
                
-               if (qfilename == "") { return processors; }
-               
                //get name of first sequence in each chunk
                map<string, int> firstSeqNames;
                for (int i = 0; i < (fastaFilePos.size()-1); i++) {
@@ -1085,59 +1083,61 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
                
                        in.close();
                }
-                               
-               //seach for filePos of each first name in the qfile and save in qfileFilePos
-               ifstream inQual;
-               m->openInputFile(qfilename, inQual);
-               
-               string input;
-               while(!inQual.eof()){   
-                       input = m->getline(inQual);
-
-                       if (input.length() != 0) {
-                               if(input[0] == '>'){ //this is a sequence name line
-                                       istringstream nameStream(input);
-                                       
-                                       string sname = "";  nameStream >> sname;
-                                       sname = sname.substr(1);
-                                       
-                                       map<string, int>::iterator it = firstSeqNames.find(sname);
-                                       
-                                       if(it != firstSeqNames.end()) { //this is the start of a new chunk
-                                               unsigned long long pos = inQual.tellg(); 
-                                               qfileFilePos.push_back(pos - input.length() - 1);       
-                                               firstSeqNames.erase(it);
-                                       }
-                               }
-                       }
-                       
-                       if (firstSeqNames.size() == 0) { break; }
-               }
-               inQual.close();
-               
-               
-               if (firstSeqNames.size() != 0) { 
-                       for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
-                               m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
-                       }
-                       qFileName = "";
-                       return processors;
-               }
-
-               //get last file position of qfile
-               FILE * pFile;
-               unsigned long long size;
-               
-               //get num bytes in file
-               pFile = fopen (qfilename.c_str(),"rb");
-               if (pFile==NULL) perror ("Error opening file");
-               else{
-                       fseek (pFile, 0, SEEK_END);
-                       size=ftell (pFile);
-                       fclose (pFile);
-               }
                
-               qfileFilePos.push_back(size);
+               if(qfilename != "")     {
+            //seach for filePos of each first name in the qfile and save in qfileFilePos
+            ifstream inQual;
+            m->openInputFile(qfilename, inQual);
+            
+            string input;
+            while(!inQual.eof()){      
+                input = m->getline(inQual);
+                
+                if (input.length() != 0) {
+                    if(input[0] == '>'){ //this is a sequence name line
+                        istringstream nameStream(input);
+                        
+                        string sname = "";  nameStream >> sname;
+                        sname = sname.substr(1);
+                        
+                        map<string, int>::iterator it = firstSeqNames.find(sname);
+                        
+                        if(it != firstSeqNames.end()) { //this is the start of a new chunk
+                            unsigned long long pos = inQual.tellg(); 
+                            qfileFilePos.push_back(pos - input.length() - 1);  
+                            firstSeqNames.erase(it);
+                        }
+                    }
+                }
+                
+                if (firstSeqNames.size() == 0) { break; }
+            }
+            inQual.close();
+            
+            
+            if (firstSeqNames.size() != 0) { 
+                for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
+                    m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
+                }
+                qFileName = "";
+                return processors;
+            }
+            
+            //get last file position of qfile
+            FILE * pFile;
+            unsigned long long size;
+            
+            //get num bytes in file
+            pFile = fopen (qfilename.c_str(),"rb");
+            if (pFile==NULL) perror ("Error opening file");
+            else{
+                fseek (pFile, 0, SEEK_END);
+                size=ftell (pFile);
+                fclose (pFile);
+            }
+            
+            qfileFilePos.push_back(size);
+        }
         
         for (int i = 0; i < (fastaFilePos.size()-1); i++) {
                        lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));