changes while testing 1.26

[mothur.git] / sequenceparser.cpp

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
index c45602e4bf5c6083ae61a5943370f58a94042260..08e5ae8b859280da965566ea9bf4d6dce3b202c7 100644 (file)
--- a/sequenceparser.cpp
+++ b/sequenceparser.cpp
@@ -64,7 +64,7 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                ifstream inName;
                m->openInputFile(nameFile, inName);
                
-               string first, second;
+               //string first, second;
                int countName = 0;
                set<string> thisnames1;
                
@@ -85,8 +85,9 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
                 
                 if (pairDone) { //save one line
+                    if (m->debug) { m->mothurOut("[DEBUG]: reading names: " + firstCol + '\t' + secondCol + ".\n"); }
                     vector<string> names;
-                    m->splitAtChar(second, names, ',');
+                    m->splitAtChar(secondCol, names, ',');
                     
                     //get aligned string for these seqs from the fasta file
                     string alignedString = "";