added save parameter to align.seqs, chimera commands, classify.seqs, and seq.error...

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index e467df11c99d735a482328c7dbe64aa623192a95..590c554b25ec761a42ecc9593d3b6376b725f15e 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "sequence.hpp"
+#include "referencedb.h"
 
 struct Compare {
        int AA, AT, AG, AC,     TA, TT, TG, TC, GA, GT, GG, GC, CA, CT, CG, CC, NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
@@ -58,6 +59,7 @@ public:
        
 private:
        bool abort;
+       ReferenceDB* rdb;
        
        struct linePair {
                unsigned long int start;
@@ -86,7 +88,7 @@ private:
 
        string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
        double threshold;
-       bool ignoreChimeras;
+       bool ignoreChimeras, save;
        int numRefs, processors;
        int maxLength, totalBases, totalMatches;
        //ofstream errorSummaryFile, errorSeqFile;