added classify.shared command and random forest files. added count file to pcr.seqs...

[mothur.git] / parsefastaqcommand.h

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index 6feabce848c09c21b2e276df8361ac4d78667f22..96fcb7d6799358ff4e10f930d1ad4165763b46a0 100644 (file)
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -23,6 +23,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "parse.fastq";         }
        string getCommandCategory()             { return "Sequence Processing"; }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
        string getDescription()         { return "reads a fastq file and creates a fasta and quality file"; }
@@ -33,10 +34,11 @@ public:
 private:
 
        vector<string> outputNames;     
-       string outputDir, fastaQFile;
+       string outputDir, fastaQFile, format;
        bool abort, fasta, qual;
        
        vector<int> convertQual(string);
+    vector<char> convertTable;
 };
 
 #endif