X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.cpp;h=2abe9ef78a8c76354d377087fa7a23deb27b4d25;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=abd3c23eaadb0001b518ac226e34148a9bcb2f07;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index abd3c23..2abe9ef 100644
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -194,12 +194,12 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
 			}else { m->setAccnosFile(accnosfile); }	
 			
 			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); } 
 								   
@@ -237,6 +237,10 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
 			
 			if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy, quality, alignreport or list."); m->mothurOutEndLine(); abort = true; }
 			
+			if ((fastafile != "") && (namefile == "")) {
+				vector<string> files; files.push_back(fastafile);
+				parser.getNameFile(files);
+			}
 		}
 
 	}
@@ -450,6 +454,9 @@ int RemoveSeqsCommand::readList(){
 		int removedCount = 0;
 		
 		while(!in.eof()){
+			
+			removedCount = 0;
+			
 			//read in list vector
 			ListVector list(in);