X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.h;h=7aaff172800c43b160fe62b2b49c2035e08502f8;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=e26e751032402cd39dac933acf3f57814ab2fc0f;hpb=90708fe9701e3827e477c82fb3652539c3bf2a0d;p=mothur.git

diff --git a/removeseqscommand.h b/removeseqscommand.h
index e26e751..7aaff17 100644
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -23,8 +23,9 @@ class RemoveSeqsCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "remove.seqs";				}
 		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getOutputFileNameTag(string, string);
+		
 	string getHelpString();	
+    string getOutputPattern(string);	
 		string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
 		string getDescription()		{ return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
 
@@ -34,12 +35,13 @@ class RemoveSeqsCommand : public Command {
 	
 	private:
 		set<string> names;
-		string accnosfile, fastafile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
+		string accnosfile, fastafile, fastqfile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
 		bool abort, dups;
 		vector<string> outputNames;
         map<string, string> uniqueMap;
 		
 		int readFasta();
+        int readFastq();
 		int readName();
 		int readGroup();
         int readCount();