Working on seq.error changes

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 6c7af2cc5a3977db356ed0806d5e4cff48e701ce..9f400b328c93aa8d03bd176283b3df17974dc0f4 100644 (file)
--- 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;