X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removeseqscommand.h;h=7aaff172800c43b160fe62b2b49c2035e08502f8;hp=151b413070bc64bafd80834e72228dabd1037c43;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=ea4f373c28543cd1002b0dd7dc6e55c526647d59

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 151b413..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"; }
 
@@ -34,11 +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();