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 a4a4215277fadbdb5857dea6d9e9319e233cad01..b5357b38e1e3bf892ef7f0cd9ffcfb7b7de4ec8a 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -33,7 +33,7 @@ private:
        bool stripQualThreshold(Sequence&, ifstream&);
        bool cullQualAverage(Sequence&, ifstream&);
        int stripBarcode(Sequence&, int&);
-       int stripForward(Sequence&);
+       int stripForward(Sequence&, int&);
        bool stripReverse(Sequence&);
        bool cullLength(Sequence&);
        bool cullHomoP(Sequence&);
@@ -45,10 +45,12 @@ private:
        string fastaFile, oligoFile, qFileName, outputDir;
        
        bool flip, allFiles, qtrim;
-       int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs;
-       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;