added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 9f8fafb24e14a807baa8dd5a981c93556c46e3b7..c019a70e4a2a7d35374192b3f8cca11787e7ecef 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -562,7 +562,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                
                int count = 0;
                bool moreSeqs = 1;
-               TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
+               TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer);
        
                while (moreSeqs) {
                                
@@ -607,6 +607,12 @@ 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);
@@ -946,7 +952,7 @@ 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, revPrimer, linker, spacer, 
+                                              pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer, 
                                              primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
                                               qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,
                                              minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap);
@@ -1187,7 +1193,6 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
                 int startIndex =  i * numSeqsPerProcessor;
                 if(i == (processors - 1)){     numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
                 lines.push_back(linePair(fastaFilePos[startIndex], numSeqsPerProcessor));
-                cout << fastaFilePos[startIndex] << '\t' << numSeqsPerProcessor << endl;
                 if (qfilename != "") {  qLines.push_back(linePair(qfileFilePos[startIndex], numSeqsPerProcessor)); }
             }
         }
@@ -1262,7 +1267,29 @@ 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 != "") {  
+                        string reverseBarcode = reverseOligo(group); //reverse barcode
+                        group = temp;
+                        
+                        //check for repeat barcodes
+                        map<string, int>::iterator itBar = rbarcodes.find(reverseBarcode);
+                        if (itBar != rbarcodes.end()) { m->mothurOut("barcode " + reverseBarcode + " is in your oligos file already."); m->mothurOutEndLine();  }
+                                               
+                        rbarcodes[reverseBarcode]=indexBarcode; 
+                    }
+                        
                                        //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();  }