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

[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index acb078173501a7d7cf48cc88f5c305e12eccc225..9e1d6f8d253e61cc22e208eaf4d68259c06d7b02 100644 (file)
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -13,7 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "chimera.h"
-
+#include "referencedb.h"
 
 /***********************************************************/
 
@@ -35,7 +35,8 @@ public:
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          
 private:
-
+       ReferenceDB* rdb;
+       
        struct linePair {
                unsigned long int start;
                unsigned long int end;
@@ -52,7 +53,7 @@ private:
        int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
        #endif
 
-       bool abort, filter;
+       bool abort, filter, save;
        string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
        int processors, window, increment, numSeqs, templateSeqsLength;
        Chimera* chimera;