X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=9b02be9ef5ec0f5a50d0563ab87a7f7d053bdadc;hb=df92022fc75c08b91cefa2c6ca4fd7b23eb480b0;hp=87b813ff9afa8575855c5cca69916de7287f9d9f;hpb=e7729bb337cfefcaba24549092cc89b44002af39;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 87b813f..9b02be9 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -34,9 +34,9 @@ private:
 	bool compareDNASeq(string, string);
 
 	bool abort;
-	string fastaFile, oligoFile, qFileName;
+	string fastaFile, oligoFile, qFileName, outputDir;
 	
-	bool flip, allFiles;
+	bool flip, allFiles, qtrim;
 	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage;
 	vector<string> forPrimer, revPrimer;
 	map<string, int> barcodes;