worked on trim.seqs

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 4a1d3d72c4f78e7c81fc22d17d996c68ff093984..a4a4215277fadbdb5857dea6d9e9319e233cad01 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -32,20 +32,20 @@ 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&);
        bool cullAmbigs(Sequence&);
        bool compareDNASeq(string, string);
-       bool compareDNASeq(string, string, int, int&);
+       int countDiffs(string, string);//, int, int&, int);
 
        bool abort;
        string fastaFile, oligoFile, qFileName, outputDir;
        
        bool flip, allFiles, qtrim;
-       int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, diffs;
+       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;