minor mods to seq.error

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 1aa133f38c379fd40c495d2c2a844de292c17f51..75a1388694284e7dedb1caee31c577cb7ce29d04 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -99,6 +99,7 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -197,6 +198,8 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }