modified trim.seqs to split by primer name if primer name is given, and warn if dupli...

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 11778fb9583f5af72b7def6c5ce421d59802dde5..b5357b38e1e3bf892ef7f0cd9ffcfb7b7de4ec8a 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -32,22 +32,25 @@ 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&, int&);
        bool stripReverse(Sequence&);
        bool cullLength(Sequence&);
        bool cullHomoP(Sequence&);
        bool cullAmbigs(Sequence&);
        bool compareDNASeq(string, string);
+       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;
-       vector<string> forPrimer, revPrimer, outputNames;
+       int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs, comboStarts;
+       vector<string> revPrimer, outputNames;
        map<string, int> barcodes;
        vector<string> groupVector;
+       map<string, int> primers;
+       map<string, int> combos;
        
        vector<int> processIDS;   //processid
        vector<linePair*> lines;