working on pam

[mothur.git] / removeseqscommand.h

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 151b413070bc64bafd80834e72228dabd1037c43..7aaff172800c43b160fe62b2b49c2035e08502f8 100644 (file)
--- 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();