X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraseqscommand.cpp;h=17f3a71a5033f1d28835bbd562af5d5f9a6b5a18;hb=fe346922fe0af5b1a025beacb211078d37598fd4;hp=ba980a50e46405dfc3087f5ba7c02d0b25cab1ff;hpb=143ce9d26deb936202317b52f6af473542c7df78;p=mothur.git

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index ba980a5..17f3a71 100644
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -52,9 +52,15 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
 			if (quanfile == "not open") { abort = true; }
 			else if (quanfile == "not found") { quanfile = "";  }
 				
-			maskfile = validParameter.validFile(parameters, "mask", true);
-			if (maskfile == "not open") { abort = true; }
-			else if (maskfile == "not found") { maskfile = "";  }	
+			maskfile = validParameter.validFile(parameters, "mask", false);
+			if (maskfile == "not found") { maskfile = "";  }	
+			else if (maskfile != "default")  { 
+				ifstream in;
+				int	ableToOpen = openInputFile(maskfile, in);
+				if (ableToOpen == 1) { abort = true; }
+				in.close();
+			}
+		
 
 			
 
@@ -129,7 +135,7 @@ int ChimeraSeqsCommand::execute(){
 			if (quanfile != "")			{		chimera->setQuantiles(quanfile);				}
 			else						{		chimera->setQuantiles("");						}
 			
-			if (maskfile == "") { mothurOut("You have not provided a mask, so I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine();  }
+			if (maskfile == "default") { mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine();  }
 			chimera->setMask(maskfile);
 						
 		}else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;		}