fixes while testing 1.33.0

[mothur.git] / makebiomcommand.h

diff --git a/makebiomcommand.h b/makebiomcommand.h
index 7ea381f145af343213a25bd32109d20fa1fb1dee..8f07c40d439529355af3fb3ee78e11b6b23aab7a 100644 (file)
--- a/makebiomcommand.h
+++ b/makebiomcommand.h
@@ -36,16 +36,19 @@ public:
        
 private:
     
-       string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label;
+       string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label, referenceTax, picrustOtuFile;
        vector<string> outputNames, Groups, sampleMetadata;
        set<string> labels;
     
-       bool abort, allLines;
+       bool abort, allLines, picrust;
     
     int getBiom(vector<SharedRAbundVector*>&);
     vector<string> getMetaData(vector<SharedRAbundVector*>&);
     vector<string> parseTax(string tax, vector<string>& scores);
     int getSampleMetaData(vector<SharedRAbundVector*>&);
+    //for picrust
+    int getGreenGenesOTUIDs(vector<SharedRAbundVector*>&, map<string, string>&);
+    map<string, string> readGGOtuMap();
 };