consensus.seqs can now find a consensus on a whole fasta file without needing a listfile

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 3c0d378f709042cc3e1c2ca2b87e730a62dbf359..7ee5c99dd86775124a83400a92f3ac1d9e24ad16 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -337,7 +337,7 @@ int TrimSeqsCommand::execute(){
                        outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
                        getOligos(fastaFileNames, qualFileNames);
                }
-               cout << fastaFileNames.size() << '\t' << qualFileNames.size() << endl;
+               
                vector<unsigned long int> fastaFilePos;
                vector<unsigned long int> qFilePos;
                
@@ -362,7 +362,6 @@ int TrimSeqsCommand::execute(){
                if (m->control_pressed) {  return 0; }                  
                                                                                
                for(int i=0;i<fastaFileNames.size();i++){
-                       cout << fastaFileNames[i] << endl;
                        
                        if (m->isBlank(fastaFileNames[i])) {  remove(fastaFileNames[i].c_str());        }
                        else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
@@ -397,7 +396,6 @@ int TrimSeqsCommand::execute(){
                
                if(qFileName != ""){
                        for(int i=0;i<qualFileNames.size();i++){
-                               cout << qualFileNames[i] << endl;
                                if (m->isBlank(qualFileNames[i])) {  remove(qualFileNames[i].c_str());  }
                                else if (filesToRemove.count(qualFileNames[i]) > 0) {  remove(qualFileNames[i].c_str()); }
                                else {
@@ -860,7 +858,7 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                //int indexPrimer = 0;
                
                while(!inOligos.eof()){
-                       inOligos >> type;
+                       inOligos >> type; m->gobble(inOligos);
                                        
                        if(type[0] == '#'){
                                while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
@@ -891,29 +889,29 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                                        map<string, int>::iterator itPrime = primers.find(oligo);
                                        if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
                                        
-                                       primers[oligo]=index; index++;
-                                       groupVector.push_back(group);
+                                               primers[oligo]=index; index++;
+                                               groupVector.push_back(group);
                                        
-                                       if(allFiles){
-                                               outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               if(qFileName != ""){
-                                                       outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                               }
-                                               if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
-                                                       filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                               if(allFiles){
+                                                       outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
                                                        if(qFileName != ""){
-                                                               filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                       }
+                                                       if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
+                                                               filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                               if(qFileName != ""){
+                                                                       filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               }
+                                                       }else {
+                                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                               outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                               if(qFileName != ""){
+                                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                                       outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               }                                                       
                                                        }
-                                               }else {
-                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                                       outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                                       if(qFileName != ""){
-                                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                               outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                       }                                                       
                                                }
-                                       }
-
+                                       
                                }
                                else if(type == "REVERSE"){
                                        Sequence oligoRC("reverse", oligo);
@@ -927,19 +925,20 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                                        map<string, int>::iterator itBar = barcodes.find(oligo);
                                        if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
                                        
-                                       barcodes[oligo]=index; index++;
-                                       groupVector.push_back(group);
+                                               barcodes[oligo]=index; index++;
+                                               groupVector.push_back(group);
+                                               
+                                               if(allFiles){
+                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                       outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                       if(qFileName != ""){
+                                                               outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                       }                                                       
+                                               }
                                        
-                                       if(allFiles){
-                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               if(qFileName != ""){
-                                                       outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                       outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                               }                                                       
-                                       }
                                }else{  m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
                        }
                        m->gobble(inOligos);