X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcurrentcommand.cpp;h=86046b64375ebd151c27e5909c0efdc9d0149bbf;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=12dcc82ff6a1bfb1a105d3d6deac903e855cea9b;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index 12dcc82..86046b6 100644
--- a/getcurrentcommand.cpp
+++ b/getcurrentcommand.cpp
@@ -138,6 +138,10 @@ int GetCurrentCommand::execute(){
 					m->setTaxonomyFile("");
 				}else if (types[i] == "flow") {
 					m->setFlowFile("");
+                }else if (types[i] == "biom") {
+					m->setBiomFile("");
+                }else if (types[i] == "count") {
+					m->setCountTableFile("");
 				}else if (types[i] == "processors") {
 					m->setProcessors("1");
 				}else if (types[i] == "all") {