added subsample and consensus parameters to unifrac.weighted command

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index f00743c546d22879f930bf25c741cdbcdd3e7fe5..b480702695a2ff6f24c7bcf6657e2f11fb3be86b 100644 (file)
--- 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();