sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / makebiomcommand.h

diff --git a/makebiomcommand.h b/makebiomcommand.h
index 9f80c2e70215b130a9020a83ce2daebb9e63a089..7ea381f145af343213a25bd32109d20fa1fb1dee 100644 (file)
--- a/makebiomcommand.h
+++ b/makebiomcommand.h
@@ -25,7 +25,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "make.biom";   }
        string getCommandCategory()             { return "General";             }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://biom-format.org/documentation/biom_format.html, http://www.mothur.org/wiki/Make.biom"; }
        string getDescription()         { return "creates a biom file"; }
     
@@ -34,8 +36,8 @@ public:
        
 private:
     
-       string sharedfile, contaxonomyfile, groups, outputDir, format, label;
-       vector<string> outputNames, Groups;
+       string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label;
+       vector<string> outputNames, Groups, sampleMetadata;
        set<string> labels;
     
        bool abort, allLines;
@@ -43,6 +45,7 @@ private:
     int getBiom(vector<SharedRAbundVector*>&);
     vector<string> getMetaData(vector<SharedRAbundVector*>&);
     vector<string> parseTax(string tax, vector<string>& scores);
+    int getSampleMetaData(vector<SharedRAbundVector*>&);
 };