modified trim.seqs to split by primer name if primer name is given, and warn if dupli...

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 7f8755645ce6664c5a299073e0ae1cbc6e875025..d2e40887851e046fe4ab23f0985c5a76b4903478 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -334,7 +334,7 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                                //find group
                                string seqGroup = groupMap->getGroup(name);
                                if (output != "accnos") {
-                                       namesOfSeqsInThisBin.push_back((name + "\t" + seqGroup + "\t" + toString(i+1)));
+                                       namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1)));
                                }else {  namesOfSeqsInThisBin.push_back(name);  }
                                
                                if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1);  }
@@ -348,7 +348,7 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                        //get last name
                        string seqGroup = groupMap->getGroup(names);
                        if (output != "accnos") {
-                               namesOfSeqsInThisBin.push_back((names + "\t" + seqGroup + "\t" + toString(i+1)));
+                               namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
                        }else {  namesOfSeqsInThisBin.push_back(names); }
                        
                        if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1);  }
@@ -379,8 +379,8 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                                        
                                        if (fastafile != "") { 
                                                if (output != "accnos") {
-                                                       string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('\t'));
-                                                       seqName = seqName.substr(0,seqName.find_last_of('\t'));
+                                                       string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));
+                                                       seqName = seqName.substr(0,seqName.find_last_of('|'));
                                                        fastaMap[seqName] = namesOfSeqsInThisBin[j];  //fastaMap needs to contain just the seq name for output later
                                                }else {
                                                        fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];