X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=c019a70e4a2a7d35374192b3f8cca11787e7ecef;hb=050e1297eaf24fabbbe0e9b76c3a5acfb90eed7d;hp=f00743c546d22879f930bf25c741cdbcdd3e7fe5;hpb=36cea83f926066127bf856e7eae1a70ce7e796d0;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index f00743c..c019a70 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -437,6 +437,17 @@ int TrimSeqsCommand::execute(){
 					
 					Sequence currSeq(in); m->gobble(in);
 					out << currSeq.getName() << '\t' << it->second << endl;
+                    
+                    if (nameFile != "") {
+                        map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+                        if (itName != nameMap.end()) { 
+                            vector<string> thisSeqsNames; 
+                            m->splitAtChar(itName->second, thisSeqsNames, ',');
+                            for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+                                out << thisSeqsNames[k] << '\t' << it->second << endl;
+                            }
+                        }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }							
+                    }
 				}
 				in.close();
 				out.close();
@@ -551,7 +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) {
 				
@@ -596,6 +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);
@@ -935,7 +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);
@@ -1176,12 +1193,10 @@ 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)); }
             }
-        
-            if(qfilename == "")	{	qLines = lines;	} //files with duds
         }
+            if(qfilename == "")	{	qLines = lines;	} //files with duds
 			return 1;
 		
 		#endif
@@ -1252,7 +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();  }