X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.cpp;fp=removelineagecommand.cpp;h=9fec2496068950b4863448fe500b17cbc957670a;hb=16abd6271c455bd01b34ff89a2e3641bef0fa128;hp=f55158fc259ace27c87d5a4fcca10e7c55539f13;hpb=896a4f281982a3c2889f6ce6d73be997072aceae;p=mothur.git

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index f55158f..9fec249 100644
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -169,12 +169,12 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
 			
 			//check for required parameters			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
-			if (fastafile == "not open") { abort = true; }
+			if (fastafile == "not open") { fastafile = ""; abort = true; }
 			else if (fastafile == "not found") {  fastafile = "";  }	
 			else { m->setFastaFile(fastafile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }
+			if (namefile == "not open") { namefile = ""; abort = true; }
 			else if (namefile == "not found") {  namefile = "";  }	
 			else { m->setNameFile(namefile); }
 			
@@ -193,7 +193,7 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
 			else { m->setListFile(listfile); }
 			
 			taxfile = validParameter.validFile(parameters, "taxonomy", true);
-			if (taxfile == "not open") { abort = true; }
+			if (taxfile == "not open") { taxfile = ""; abort = true; }
 			else if (taxfile == "not found") {  		
 				taxfile = m->getTaxonomyFile(); 
 				if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
@@ -220,7 +220,12 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
 			if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
 		
 			if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }			
-
+			
+			if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+				vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+				parser.getNameFile(files);
+			}
+			
 		}
 
 	}