X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;fp=chimeraccodecommand.cpp;h=bc96e0530993e63cf099381a1ccd8829f9cc7714;hb=220dc345e493cddc569521111ce32ac4d965ab7f;hp=df4e67db118462e1115857331c7adcc4551a272c;hpb=23e60689fa4306234b3d05b116f25d198316d1ae;p=mothur.git

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index df4e67d..bc96e05 100644
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -185,6 +185,8 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
 							//erase from file list
 							fastaFileNames.erase(fastaFileNames.begin()+i);
 							i--;
+						}else {
+							m->setFastaFile(fastaFileNames[i]);
 						}
 					}
 				}