changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 67f6b57be1a64f9ae760c86258cea67cdbd62f02..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");