testing 1.22.0

[mothur.git] / sequenceparser.cpp

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
index e60f19b0df0034de0c1a693d7c5a55c59ef0ef82..76c90c3f9eb7f2802276526c8491dee1d1ba3883 100644 (file)
--- a/sequenceparser.cpp
+++ b/sequenceparser.cpp
@@ -63,6 +63,7 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                
                string first, second;
                int countName = 0;
+               set<string> thisnames1;
                while(!inName.eof()) {
                        
                        if (m->control_pressed) { break; }
@@ -94,10 +95,12 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                                        it = splitMap.find(group);
                                        if (it != splitMap.end()) { //adding seqs to this group
                                                (it->second) += "," + names[i];
+                                               thisnames1.insert(names[i]);
                                                countName++;
                                        }else { //first sighting of this group
                                                splitMap[group] = names[i];
                                                countName++;
+                                               thisnames1.insert(names[i]);
                                                
                                                //is this seq in the fasta file?
                                                if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
@@ -131,6 +134,13 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                if (error == 1) { m->control_pressed = true; }
                
                if (countName != (groupMap->getNumSeqs())) {
+                       vector<string> groupseqsnames = groupMap->getNamesSeqs();
+                       for (int i = 0; i < groupseqsnames.size(); i++) {
+                               set<string>::iterator itnamesfile = thisnames1.find(groupseqsnames[i]);
+                               if (itnamesfile == thisnames1.end()){
+                                       cout << "missing name " + groupseqsnames[i] << '\t' << allSeqsMap[groupseqsnames[i]] << endl;
+                               }
+                       }
                        m->mothurOutEndLine();
                        m->mothurOut("[ERROR]: Your name file contains " + toString(countName) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
                        m->mothurOutEndLine();