X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=a4a4215277fadbdb5857dea6d9e9319e233cad01;hb=2bb20fb79f19b8bda48492d89f8e8b7389431413;hp=11778fb9583f5af72b7def6c5ce421d59802dde5;hpb=c9c6df74a855bc1fcecb93cf56eb09d0907e7cf2;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 11778fb..a4a4215 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -32,19 +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);
+	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;
+	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;