X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.h;h=9f400b328c93aa8d03bd176283b3df17974dc0f4;hb=0a9b5ee954b60abbd24c797cece23fb4a487cc8a;hp=6c7af2cc5a3977db356ed0806d5e4cff48e701ce;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e;p=mothur.git

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 6c7af2c..9f400b3 100644
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -92,7 +92,7 @@ private:
 
 	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
 	double threshold;
-	bool ignoreChimeras, save;
+	bool ignoreChimeras, save, aligned;
 	int numRefs, processors;
 	int maxLength, totalBases, totalMatches;
 	//ofstream errorSummaryFile, errorSeqFile;