X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=9f8fafb24e14a807baa8dd5a981c93556c46e3b7;hb=8a0b2fd6644dee848b262fcdea73b912a6054fed;hp=5d4eb39d16f3bdc575a3ee41125705c90da9824f;hpb=57b3c96832667c1b70d4d526331f52e3d49e8237;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 5d4eb39..9f8fafb 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -329,6 +329,8 @@ int TrimSeqsCommand::execute(){
 		
 		numFPrimers = 0;  //this needs to be initialized
 		numRPrimers = 0;
+        numSpacers = 0;
+        numLinkers = 0;
 		createGroup = false;
 		vector<vector<string> > fastaFileNames;
 		vector<vector<string> > qualFileNames;
@@ -435,6 +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();
@@ -1177,9 +1190,8 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
                 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