finished chimera changes

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index d34149d1e74fb8738a89133fc9e343268ef9121f..1758cf682fad21efcd0201b0b50b0ada7857d100 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -315,20 +315,12 @@ int ChimeraSeqsCommand::execute(){
                string accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + method + maskfile + ".accnos";
 
                
-               vector<Sequence*> templateSeqs;
                if ((method != "bellerophon") && (method != "chimeracheck")) {   
-                       templateSeqs = chimera->readSeqs(templatefile);   
                        if (chimera->getUnaligned()) { 
                                mothurOut("Your template sequences are different lengths, please correct."); mothurOutEndLine(); 
-                               //free memory
-                               for (int i = 0; i < templateSeqs.size(); i++)           {  delete templateSeqs[i];              }
                                delete chimera;
                                return 0; 
                        }
-                       
-                       //set options
-                       chimera->setTemplateSeqs(templateSeqs);
-
                }else if (method == "bellerophon") {//run bellerophon separately since you need to read entire fastafile to run it
                        chimera->getChimeras();
                        
@@ -435,7 +427,6 @@ int ChimeraSeqsCommand::execute(){
                remove(outputFileName.c_str());
                rename(tempHeader.c_str(), outputFileName.c_str());
        
-               for (int i = 0; i < templateSeqs.size(); i++)           {  delete templateSeqs[i];      } 
                delete chimera;
                
                if (method == "chimeracheck") { remove(accnosFileName.c_str());  mothurOutEndLine(); mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); mothurOutEndLine();  }