X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=globaldata.cpp;h=a3dc757cba2e9adf6aecc051f3a03d9875b92026;hb=e7fe6dd9db877b98c362f9524c3130bbbd037200;hp=c42969e5ff5b8450a5ae63e9876e0f5bde8d29ad;hpb=bffbd9ad0d837bc9523d95e7b35c34cfd2631046;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index c42969e..a3dc757 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -44,8 +44,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			cutoff = "1.0";
 		}
 		
-		//set default value for cutoff
-		if(commandName == "dist.seqs") {	cutoff = "1.0";		}
+		//set default value for cutoff and phylip
+		if (commandName == "dist.seqs") {	cutoff = "1.0";	  phylipfile = "F";	}
 
 		string key, value;		
 		//reads in parameters and values
@@ -208,9 +208,12 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 		}
 		
 		//set format for shared
-		if((listfile != "") && (groupfile != "")) { format = "shared"; }
-		if((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
-				
+		if ((listfile != "") && (groupfile != "")) { format = "shared"; }
+		if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
+		
+		//set default value for cutoff
+		if (commandName == "dist.seqs") {	format = "fasta";  inputFileName = fastafile;  fileroot = fastafile;	}
+						
 		//input defaults for calculators
 		if(commandName == "collect.single") {