X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;h=9bf188db3d25fa4ac16b82973a2802c3b1e6ad75;hb=50b8969afdc29f038b0fb73a528e51220cb87f19;hp=ffe49b48810d7916e5324efd9480c87e8322ec92;hpb=8742edef7a51b82834289e570d336f5a81ba1f2b;p=mothur.git

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index ffe49b4..9bf188d 100644
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -206,12 +206,12 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
 			if (accnosfile2 == "not found") { accnosfile2 = ""; }
 			
 			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); }
 			
@@ -230,7 +230,7 @@ GetSeqsCommand::GetSeqsCommand(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 = "";  }
 			else { m->setTaxonomyFile(taxfile); }
 			
@@ -249,6 +249,11 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
 			dups = m->isTrue(temp);
 			
 			if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (accnosfile2 == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; }
+		
+			if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+				vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+				parser.getNameFile(files);
+			}
 		}
 
 	}