X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=seqerrorcommand.h;h=aac17b6979910ebc733be840eb37ec720ecc1105;hp=6c7af2cc5a3977db356ed0806d5e4cff48e701ce;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 6c7af2c..aac17b6 100644
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -13,6 +13,7 @@
 #include "command.hpp"
 #include "sequence.hpp"
 #include "referencedb.h"
+#include "counttable.h"
 
 
 class SeqErrorCommand : public Command {
@@ -90,9 +91,9 @@ private:
 	int driver(string, string, string, string, string, string, linePair, linePair, linePair);
 	int createProcesses(string, string, string, string, string, string);
 
-	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
+	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir, countfile;
 	double threshold;
-	bool ignoreChimeras, save;
+	bool ignoreChimeras, save, aligned;
 	int numRefs, processors;
 	int maxLength, totalBases, totalMatches;
 	//ofstream errorSummaryFile, errorSeqFile;