fixed pintail bug

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 69eb89533b4988e598c000b8bf5b8a111e07e5e1..668956f838306c2e3bbb0eb0a06b7089a228960d 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -90,7 +90,7 @@ void ChimeraBellerophonCommand::help(){
                m->mothurOut("The chimera.bellerophon command reads a fastafile and creates list of potentially chimeric sequences.\n");
                m->mothurOut("The chimera.bellerophon command parameters are fasta, filter, correction, processors, window, increment. The fasta parameter is required.\n");
                m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter, default=false. \n");
-               m->mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs.\n");
+               m->mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs, default=true.\n");
                m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
                #ifdef USE_MPI
                m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
@@ -136,18 +136,23 @@ int ChimeraBellerophonCommand::execute(){
                
                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                                                
-               char* outFilename = new char[accnosFileName.length()];\r
-               memcpy(outFilename, accnosFileName.c_str(), accnosFileName.length());
-
-               char* FileName = new char[outputFileName.length()];\r
-               memcpy(FileName, outputFileName.c_str(), outputFileName.length());
+               //char* outFilename = new char[accnosFileName.length()];
+               //memcpy(outFilename, accnosFileName.c_str(), accnosFileName.length());
+               
+               char outFilename[1024];
+               strcpy(outFilename, accnosFileName.c_str());
 
+               //char* FileName = new char[outputFileName.length()];
+               //memcpy(FileName, outputFileName.c_str(), outputFileName.length());
+               
+               char FileName[1024];
+               strcpy(FileName, outputFileName.c_str());
 
                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);
                
-               delete FileName;
-               delete outFilename;
+               //delete FileName;
+               //delete outFilename;
 
                numSeqs = chimera->print(outMPI, outMPIAccnos);