added modify names parameter to set.dir

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 935b9a9297e08d1f50e89d4b9a059cf9cbe8e54a..16d83de2596b9cf84ab4069789917878fa89559e 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -422,7 +422,7 @@ int TrimSeqsCommand::execute(){
                
                if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, true);
             nameCount = ct.getNameMap();
                        outputNames.push_back(trimCountFile);
                        outputNames.push_back(scrapCountFile);
@@ -443,7 +443,9 @@ int TrimSeqsCommand::execute(){
                                outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
                        }
                }
-       
+        
+        if (!pairedOligos) { if (reorient) { m->mothurOut("[WARNING]: You cannot use reorient without paired barcodes or primers, skipping."); m->mothurOutEndLine(); reorient = false; } }
+        
         if (m->control_pressed) { return 0; }
             
         //fills lines and qlines
@@ -538,7 +540,7 @@ int TrimSeqsCommand::execute(){
             
             if (countfile != "") { //create countfile with group info included
                 CountTable* ct = new CountTable();
-                ct->readTable(trimCountFile);
+                ct->readTable(trimCountFile, true);
                 map<string, int> justTrimmedNames = ct->getNameMap();
                 delete ct;
                 
@@ -738,7 +740,9 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                 
                                if(numBarcodes != 0){
                                        success = trimOligos->stripBarcode(currSeq, currQual, barcodeIndex);
-                                       if(success > bdiffs)            {       trashCode += 'b';       }
+                                       if(success > bdiffs)            {
+                        trashCode += 'b';
+                    }
                                        else{ currentSeqsDiffs += success;  }
                                }
                                
@@ -752,9 +756,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                if(numFPrimers != 0){
                                        success = trimOligos->stripForward(currSeq, currQual, primerIndex, keepforward);
                                        if(success > pdiffs)            {
-                        //if (pairedOligos) {  trashCode += trimOligos->getTrashCode(); }
-                        //else {  trashCode += 'f';  }
-                        trashCode += 'f';
+                          trashCode += 'f';  
                     }
                                        else{ currentSeqsDiffs += success;  }
                                }
@@ -776,17 +778,13 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                     
                     if(numBarcodes != 0){
                         thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
-                        if(thisSuccess > bdiffs)               {       thisTrashCode += 'b';   }
+                        if(thisSuccess > bdiffs)               { thisTrashCode += "b"; }
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
                     
                     if(numFPrimers != 0){
                         thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, keepforward);
-                            if(thisSuccess > pdiffs)           {
-                            //if (pairedOligos) {  thisTrashCode += rtrimOligos->getTrashCode(); }
-                            //else {  thisTrashCode += 'f';  }
-                            thisTrashCode += 'f'; 
-                        }
+                        if(thisSuccess > pdiffs)               { thisTrashCode += "f"; }
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
                    
@@ -804,7 +802,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                             savedQual.flipQScores();
                             currQual.setScores(savedQual.getScores());
                         }
-                    }
+                    }else { trashCode += "(" + thisTrashCode + ")";  }
                 }
                 
                                if(keepFirst != 0){
@@ -1393,9 +1391,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
                         string sname = "";  nameStream >> sname;
                         sname = sname.substr(1);
                         
-                        for (int i = 0; i < sname.length(); i++) {
-                            if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
-                        }
+                        m->checkName(sname);
                         
                         map<string, int>::iterator it = firstSeqNames.find(sname);
                         
@@ -1535,7 +1531,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                                                char c = inOligos.get(); 
-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        } 
@@ -1650,10 +1646,10 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
         if (hasPairedBarcodes || hasPrimer) {
             pairedOligos = true;
             if ((primers.size() != 0) || (barcodes.size() != 0) || (linker.size() != 0) || (spacer.size() != 0) || (revPrimer.size() != 0)) { m->control_pressed = true;  m->mothurOut("[ERROR]: cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting."); m->mothurOutEndLine();  return 0; }
-        }
+        }else if (reorient) { m->mothurOut("[Warning]: cannot use checkorient without paired barcodes or primers, ignoring.\n"); m->mothurOutEndLine(); reorient = false; }
         
                if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
-               
+        
                //add in potential combos
                if(barcodeNameVector.size() == 0){
                        barcodes[""] = 0;
@@ -1854,7 +1850,13 @@ bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
                if(qscores.getName() != ""){
                        qscores.trimQScores(-1, keepFirst);
                }
+
+//        sequence.printSequence(cout);cout << endl;
+        
                sequence.trim(keepFirst);
+        
+//        sequence.printSequence(cout);cout << endl << endl;;
+
                return success;
        }
        catch(exception& e) {