X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;fp=chimeracheckcommand.cpp;h=5b249d7ff6892a53ce0493c3fa5319468681a8bd;hb=220dc345e493cddc569521111ce32ac4d965ab7f;hp=d82a84a1b86ab5643e0416d8d73091ce16b29e23;hpb=23e60689fa4306234b3d05b116f25d198316d1ae;p=mothur.git

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index d82a84a..5b249d7 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -183,6 +183,8 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
 							//erase from file list
 							fastaFileNames.erase(fastaFileNames.begin()+i);
 							i--;
+						}else {
+							m->setFastaFile(fastaFileNames[i]);
 						}
 					}
 				}
@@ -262,6 +264,8 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
 							//erase from file list
 							nameFileNames.erase(nameFileNames.begin()+i);
 							i--;
+						}else {
+							m->setNameFile(nameFileNames[i]);
 						}
 					}
 				}