X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.cpp;h=c50255aeb2ae9c202074b78d89d460651cefdc43;hb=5c5c0428f6d548c28a8b903ac80efed4f92d59db;hp=2d77d28d367c8c9cf0be0e8b0094817f4adb1ee9;hpb=b866e1519a60681527244036428104ad1cb90c93;p=mothur.git

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 2d77d28..c50255a 100644
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -118,7 +118,7 @@ SffInfoCommand::SffInfoCommand(){
 SffInfoCommand::SffInfoCommand(string option)  {
 	try {
 		abort = false; calledHelp = false;   
-		hasAccnos = false;
+		hasAccnos = false; hasOligos = false;
         split = 1;
 		
 		//allow user to run help
@@ -583,7 +583,6 @@ int SffInfoCommand::extractSffInfo(string input, string accnos, string oligos){
             //create new common headers for each file with the correct number of reads
             adjustCommonHeader(header);
             
-            map<string, string> uniqueSffNames;// so we don't add the same sff multiple times
 			map<string, string>::iterator it;
 			set<string> namesToRemove;
 			for(int i=0;i<filehandles.size();i++){
@@ -594,12 +593,7 @@ int SffInfoCommand::extractSffInfo(string input, string accnos, string oligos){
 								m->mothurRemove(filehandles[i][j]);
                                 m->mothurRemove(filehandlesHeaders[i][j]);
 								namesToRemove.insert(filehandles[i][j]);
-                            }else{	
-								it = uniqueSffNames.find(filehandles[i][j]);
-								if (it == uniqueSffNames.end()) {	
-									uniqueSffNames[filehandles[i][j]] = barcodeNameVector[i];	
-								}	
-							}
+                            }
 						}
 					}
 				}
@@ -1043,7 +1037,7 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, H
 int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& primer) {
 	try {
         //find group read belongs to
-        TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer);
+        TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
         
         int success = 1;
         string trashCode = "";
@@ -1088,12 +1082,6 @@ int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& pr
             else{ currentSeqsDiffs += success;  }
         }
         
-        if(rbarcodes.size() != 0){
-            success = trimOligos.stripRBarcode(currSeq, currQual, barcode);
-            if(success > bdiffs)		{	trashCode += 'b';	}
-            else{ currentSeqsDiffs += success;  }
-        }
-        
         if(numSpacers != 0){
             success = trimOligos.stripSpacer(currSeq, currQual);
             if(success > sdiffs)		{	trashCode += 's';	}
@@ -1681,36 +1669,13 @@ bool SffInfoCommand::readOligos(string oligoFile){
 				}
 				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();  }
                     
 					barcodes[oligo]=indexBarcode; indexBarcode++;
 					barcodeNameVector.push_back(group);
-
 				}else if(type == "LINKER"){
 					linker.push_back(oligo);
 				}else if(type == "SPACER"){