X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.h;h=7aaff172800c43b160fe62b2b49c2035e08502f8;hb=2ff2d03fbe46ce8cf2738bff4403a52be4f31e2f;hp=d99151ec022dfdafcfa2327998466549cbcb3eda;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/removeseqscommand.h b/removeseqscommand.h
index d99151e..7aaff17 100644
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -23,23 +23,29 @@ class RemoveSeqsCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "remove.seqs";				}
 		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getHelpString();	
-	
+		
+	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"; }
+
 		int execute(); 
 		void help() { m->mothurOut(getHelpString()); }	
 	
 	
 	private:
 		set<string> names;
-		string accnosfile, fastafile, namefile, groupfile, 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();
 		int readAlign();
-		void readAccnos();
 		int readList();
 		int readTax();
 		int readQual();