added dups parameter to chimera.uchime. working on make.contigs command.

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index bbb0b367a59de85b94e6dd9e561b697d37832b00..0c21c8993552929a5299841a5089783f7b8c2aef 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -660,7 +660,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                
                int count = 0;
                bool moreSeqs = 1;
-               TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer);
+               TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
        
                while (moreSeqs) {
                                
@@ -704,12 +704,6 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                        if(success > bdiffs)            {       trashCode += 'b';       }
                                        else{ currentSeqsDiffs += success;  }
                                }
-                
-                if(rbarcodes.size() != 0){
-                                       success = trimOligos.stripRBarcode(currSeq, currQual, barcodeIndex);
-                                       if(success > bdiffs)            {       trashCode += 'b';       }
-                                       else{ currentSeqsDiffs += success;  }
-                               }
                                
                 if(numSpacers != 0){
                                        success = trimOligos.stripSpacer(currSeq, currQual);
@@ -1088,7 +1082,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                               tempPrimerQualFileNames,
                                               tempNameFileNames,
                                               lines[i].start, lines[i].end, qLines[i].start, qLines[i].end, m,
-                                              pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer, 
+                                              pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, revPrimer, linker, spacer, 
                                              primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
                                               qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,
                                              minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap, nameCount);
@@ -1435,40 +1429,11 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                }
                                else if(type == "BARCODE"){
                                        inOligos >> group;
-                    
-                    //barcode lines can look like   BARCODE   atgcatgc   groupName  - for 454 seqs
-                    //or                            BARCODE   atgcatgc   atgcatgc    groupName  - for illumina data that has forward and reverse info
-                                       string temp = "";
-                    while (!inOligos.eof())    {       
-                                               char c = inOligos.get(); 
-                                               if (c == 10 || c == 13){        break;  }
-                                               else if (c == 32 || c == 9){;} //space or tab
-                                               else {  temp += c;  }
-                                       } 
                                        
-                    //then this is illumina data with 4 columns
-                    if (temp != "") {  
-                        
-                        for(int i=0;i<group.length();i++){
-                            group[i] = toupper(group[i]);
-                            if(group[i] == 'U')        {       group[i] = 'T'; }
-                        }
-                        
-                        if (m->debug) { m->mothurOut("[DEBUG]: reading reverse " + group + ", and group = " + temp + ".\n"); }
-                        
-                        string reverseBarcode = reverseOligo(group); //reverse barcode
-                        //check for repeat barcodes
-                        map<string, int>::iterator itBar = rbarcodes.find(reverseBarcode);
-                        if (itBar != rbarcodes.end()) { m->mothurOut("reverse barcode " + group + " is in your oligos file already."); m->mothurOutEndLine();  }
-                        
-                        group = temp;
-                        rbarcodes[reverseBarcode]=indexBarcode; 
-                    }else { if (m->debug) { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); } }
-                        
                                        //check for repeat barcodes
                                        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]=indexBarcode; indexBarcode++;
                                        barcodeNameVector.push_back(group);
                                }else if(type == "LINKER"){