added name option to read.tree for use in unifrac and parimony commands

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index ee79d777a8d11ffaa2e279e69463314f9c3b8938..9b02be9ef5ec0f5a50d0563ab87a7f7d053bdadc 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -22,7 +22,7 @@ public:
        void help();
        
 private:
-       void getOligos(vector<ofstream*>&, vector<ofstream*>&);
+       void getOligos(vector<ofstream*>&);
        bool stripQualThreshold(Sequence&, ifstream&);
        bool cullQualAverage(Sequence&, ifstream&);
        bool stripBarcode(Sequence&, int&);
@@ -34,9 +34,9 @@ private:
        bool compareDNASeq(string, string);
 
        bool abort;
-       string fastaFile, oligoFile, qFileName;
+       string fastaFile, oligoFile, qFileName, outputDir;
        
-       bool flip, allFiles;
+       bool flip, allFiles, qtrim;
        int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage;
        vector<string> forPrimer, revPrimer;
        map<string, int> barcodes;