changes while testing

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 6c7af2cc5a3977db356ed0806d5e4cff48e701ce..aac17b6979910ebc733be840eb37ec720ecc1105 100644 (file)
--- 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;