sped up the remove.seqs and remove.lineage and get.seqs and get.lineage. fixed bug...

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index a331908c1ddb09609d469ceb186ce659f1e21f08..9b4a87b6a45124d5e472952626207e82e1ebbb67 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -569,6 +569,20 @@ int ChimeraSlayerCommand::execute(){
                        m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
                }
                
+               //set accnos file as new current accnosfile
+               string current = "";
+               itTypes = outputTypes.find("accnos");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+               }
+               
+               if (trim) {
+                       itTypes = outputTypes.find("fasta");
+                       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();    }       
@@ -670,7 +684,7 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f
                                        
                                        
                                }
-                       count++;
+                               count++;
                        }
                        delete candidateSeq;