fixed some bugs found while testing 1.8

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 7af1ac67349843c59a282338387dc127239a1bcb..049758943550859e7df4a933ea427421be450e85 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -189,7 +189,7 @@ int GetSharedOTUCommand::execute(){
                        openInputFile(fastafile, inFasta);
                        
                        while(!inFasta.eof()) {
-                               Sequence seq(inFasta);
+                               Sequence seq(inFasta); gobble(inFasta);
                                if (seq.getName() != "") {  seqs.push_back(seq);   }
                        }
                        inFasta.close();
@@ -404,7 +404,7 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                                        }
                                        
                                        outFasta << seqs[k].getAligned() << endl;
-                               }else {         mothurOut(seqs[k].getName() + " is not in your fasta file. Please correct."); mothurOutEndLine();       }
+                               }
                        }
                        
                        outFasta.close();