modified trim.seqs to account for primers of different lengths

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 11778fb9583f5af72b7def6c5ce421d59802dde5..f9a251c9323a9388af285ce6933fd5b676fe3838 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -39,12 +39,13 @@ private:
        bool cullHomoP(Sequence&);
        bool cullAmbigs(Sequence&);
        bool compareDNASeq(string, string);
+       bool compareDNASeq(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;
+       int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs, currentSeqsTdiffs;
        vector<string> forPrimer, revPrimer, outputNames;
        map<string, int> barcodes;
        vector<string> groupVector;