working on chimera.uchime change for dereplicate=t bug. added shared file to get...

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 0a6eae93df72e8556554bef32c5a52074a4d0a54..641a3abce04bde1b8002e11af636fcd5e58bc6e2 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -407,6 +407,13 @@ int SeqErrorCommand::execute(){
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");
                m->mothurOutEndLine();
                
+        //set fasta file as new current fastafile
+               string current = "";
+               itTypes = outputTypes.find("errorseq");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+               }
+        
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }