X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=a4a4215277fadbdb5857dea6d9e9319e233cad01;hb=e21aedb9ffeabff18207d53e9cc5420d2e30a5b2;hp=4a1d3d72c4f78e7c81fc22d17d996c68ff093984;hpb=c7f1abdd8b8d24f186320880515a848039ce051a;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 4a1d3d7..a4a4215 100644
--- 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;