worked on trim.seqs

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index f944e7f6cd197674ad36b4cf6d3b9209b473f2e7..a4a4215277fadbdb5857dea6d9e9319e233cad01 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -32,8 +32,8 @@ private:
        void getOligos(vector<string>&);
        bool stripQualThreshold(Sequence&, ifstream&);
        bool cullQualAverage(Sequence&, ifstream&);
-       bool stripBarcode(Sequence&, int&);
-       bool stripForward(Sequence&);
+       int stripBarcode(Sequence&, int&);
+       int stripForward(Sequence&);
        bool stripReverse(Sequence&);
        bool cullLength(Sequence&);
        bool cullHomoP(Sequence&);
@@ -45,7 +45,7 @@ private:
        string fastaFile, oligoFile, qFileName, outputDir;
        
        bool flip, allFiles, qtrim;
-       int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs, currentSeqsTdiffs;
+       int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs;
        vector<string> forPrimer, revPrimer, outputNames;
        map<string, int> barcodes;
        vector<string> groupVector;