X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=f9a251c9323a9388af285ce6933fd5b676fe3838;hb=17aafaea968f87e581297063b16695ad515bea53;hp=4a1d3d72c4f78e7c81fc22d17d996c68ff093984;hpb=763612fc464c6183b0d0fa8742ad1fa30fc04df5;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 4a1d3d7..f9a251c 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -39,13 +39,13 @@ private:
 	bool cullHomoP(Sequence&);
 	bool cullAmbigs(Sequence&);
 	bool compareDNASeq(string, string);
-	bool compareDNASeq(string, string, int, int&);
+	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, diffs;
+	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;