working on chimera change to add trim feature, fixed bug in print of distance file...

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 34096159b4e1379d5e7c61ea6094d8514d48267c..5d7d6d452b2c741ad764623557f0a0d31895ba0e 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -53,6 +53,7 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(){
                vector<string> tempOutNames;
                outputTypes["chimera"] = tempOutNames;
                outputTypes["accnos"] = tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
@@ -87,6 +88,7 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                        vector<string> tempOutNames;
                        outputTypes["chimera"] = tempOutNames;
                        outputTypes["accnos"] = tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
                
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -241,7 +243,7 @@ int ChimeraBellerophonCommand::execute(){
                        MPI_File_open(MPI_COMM_WORLD, FileName, outMode, MPI_INFO_NULL, &outMPI);  //comm, filename, mode, info, filepointer
                        MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
        
-                       numSeqs = chimera->print(outMPI, outMPIAccnos);
+                       numSeqs = chimera->print(outMPI, outMPIAccnos, "");
                        
                        MPI_File_close(&outMPI);
                        MPI_File_close(&outMPIAccnos);
@@ -254,7 +256,7 @@ int ChimeraBellerophonCommand::execute(){
                        ofstream out2;
                        m->openOutputFile(accnosFileName, out2);
                        
-                       numSeqs = chimera->print(out, out2);
+                       numSeqs = chimera->print(out, out2, "");
                        out.close();
                        out2.close();