added ignore option to oligos files for make.contigs, trim.seqs, trim.flows

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 60d29f9e56024de7a0d6d39478ce12872788acd5..891b14dc463342e9403aab317fc0877fdd78e82c 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -395,29 +395,8 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                }
                                
                                if(trashCode.length() == 0){
-                                       currSeq.setAligned(currSeq.getUnaligned());
-                                       currSeq.printSequence(trimFASTAFile);
-                                       
-                                       if(pDataArray->qFileName != ""){
-                                               currQual.printQScores(trimQualFile);
-                                       }
-                                       
-                                       if(pDataArray->nameFile != ""){
-                                               map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
-                                               if (itName != pDataArray->nameMap.end()) {  trimNameFile << itName->first << '\t' << itName->second << endl; }
-                                               else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
-                                       }
-                                       
-                    int numRedundants = 0;
-                    if (pDataArray->countfile != "") {
-                        map<string, int>::iterator itCount = pDataArray->nameCount.find(currSeq.getName());
-                        if (itCount != pDataArray->nameCount.end()) { 
-                            trimCountFile << itCount->first << '\t' << itCount->second << endl;
-                            numRedundants = itCount->second-1;
-                        }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); pDataArray->m->mothurOutEndLine(); }
-                    }
-                                       
-                                       if (pDataArray->createGroup) {
+                    string thisGroup = "";
+                    if (pDataArray->createGroup) {
                                                if(pDataArray->barcodes.size() != 0){
                                                        string thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
                                                        if (pDataArray->primers.size() != 0) { 
@@ -429,50 +408,81 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                                                        }
                                                                } 
                                                        }
-                                                       
-                                                       if (pDataArray->countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; }
-                            else {   pDataArray->groupMap[currSeq.getName()] = thisGroup; }
-                                                       
-                                                       if (pDataArray->nameFile != "") {
-                                                               map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
-                                                               if (itName != pDataArray->nameMap.end()) { 
-                                                                       vector<string> thisSeqsNames; 
-                                                                       pDataArray->m->splitAtChar(itName->second, thisSeqsNames, ',');
-                                    numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
-                                                                       for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
-                                                                               outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
-                                                                       }
-                                                               }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }                                                   
-                                                       }
-                                                       
-                                                       map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
-                                                       if (it == pDataArray->groupCounts.end()) {      pDataArray->groupCounts[thisGroup] = 1 + numRedundants; }
-                                                       else { pDataArray->groupCounts[it->first] += (1 + numRedundants); }
+                        }
+                    }
+                    
+                    int pos = thisGroup.find("ignore");
+                    if (pos == string::npos) {
+                        
+                        currSeq.setAligned(currSeq.getUnaligned());
+                        currSeq.printSequence(trimFASTAFile);
+                        
+                        if(pDataArray->qFileName != ""){
+                            currQual.printQScores(trimQualFile);
+                        }
+                        
+                        if(pDataArray->nameFile != ""){
+                            map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
+                            if (itName != pDataArray->nameMap.end()) {  trimNameFile << itName->first << '\t' << itName->second << endl; }
+                            else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
+                        }
+                        
+                        int numRedundants = 0;
+                        if (pDataArray->countfile != "") {
+                            map<string, int>::iterator itCount = pDataArray->nameCount.find(currSeq.getName());
+                            if (itCount != pDataArray->nameCount.end()) { 
+                                trimCountFile << itCount->first << '\t' << itCount->second << endl;
+                                numRedundants = itCount->second-1;
+                            }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); pDataArray->m->mothurOutEndLine(); }
+                        }
+                        
+                        if (pDataArray->createGroup) {
+                            if(pDataArray->barcodes.size() != 0){
+                                
+                                if (pDataArray->countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; }
+                                else {   pDataArray->groupMap[currSeq.getName()] = thisGroup; }
+                                
+                                if (pDataArray->nameFile != "") {
+                                    map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
+                                    if (itName != pDataArray->nameMap.end()) { 
+                                        vector<string> thisSeqsNames; 
+                                        pDataArray->m->splitAtChar(itName->second, thisSeqsNames, ',');
+                                        numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
+                                        for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+                                            outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
+                                        }
+                                    }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }                                                      
+                                }
+                                
+                                map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
+                                if (it == pDataArray->groupCounts.end()) {     pDataArray->groupCounts[thisGroup] = 1 + numRedundants; }
+                                else { pDataArray->groupCounts[it->first] += (1 + numRedundants); }
+                                
+                            }
+                        }
+                        
+                        if(pDataArray->allFiles){
+                            ofstream output;
+                            pDataArray->m->openOutputFileAppend(pDataArray->fastaFileNames[barcodeIndex][primerIndex], output);
+                            currSeq.printSequence(output);
+                            output.close();
                             
-                                               }
-                                       }
-                                       
-                                       if(pDataArray->allFiles){
-                                               ofstream output;
-                                               pDataArray->m->openOutputFileAppend(pDataArray->fastaFileNames[barcodeIndex][primerIndex], output);
-                                               currSeq.printSequence(output);
-                                               output.close();
-                                               
-                                               if(pDataArray->qFileName != ""){
-                                                       pDataArray->m->openOutputFileAppend(pDataArray->qualFileNames[barcodeIndex][primerIndex], output);
-                                                       currQual.printQScores(output);
-                                                       output.close();                                                 
-                                               }
-                                               
-                                               if(pDataArray->nameFile != ""){
-                                                       map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
-                                                       if (itName != pDataArray->nameMap.end()) { 
-                                                               pDataArray->m->openOutputFileAppend(pDataArray->nameFileNames[barcodeIndex][primerIndex], output);
-                                                               output << itName->first << '\t' << itName->second << endl; 
-                                                               output.close();
-                                                       }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
-                                               }
-                                       }
+                            if(pDataArray->qFileName != ""){
+                                pDataArray->m->openOutputFileAppend(pDataArray->qualFileNames[barcodeIndex][primerIndex], output);
+                                currQual.printQScores(output);
+                                output.close();                                                        
+                            }
+                            
+                            if(pDataArray->nameFile != ""){
+                                map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
+                                if (itName != pDataArray->nameMap.end()) { 
+                                    pDataArray->m->openOutputFileAppend(pDataArray->nameFileNames[barcodeIndex][primerIndex], output);
+                                    output << itName->first << '\t' << itName->second << endl; 
+                                    output.close();
+                                }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
+                            }
+                        }
+                    }
                                }
                                else{
                                        if(pDataArray->nameFile != ""){ //needs to be before the currSeq name is changed