X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensusseqscommand.h;h=423c4e48796a2a9294dc8373fd29823b3418abb0;hb=e0b6040c7b6ad4ecdad4aa90b4326c0528379178;hp=226b4c959bf25f9c0629a556755641809401baa4;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index 226b4c9..423c4e4 100644
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -1,6 +1,6 @@
 #ifndef CONSENSUSSEQSCOMMAND_H
 #define CONSENSUSSEQSCOMMAND_H
-
+//test
 /*
  *  consensusseqscommand.h
  *  Mothur
@@ -25,6 +25,8 @@ public:
 	string getCommandCategory()		{ return "Sequence Processing"; }
 	string getHelpString();	
 	string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
+	string getDescription()		{ return "create a consensus sequence for each OTU or for a fasta file"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -38,12 +40,13 @@ private:
 	map<string, string> fastaMap;
 	map<string, string> nameMap;
 	map<string, string> nameFileMap;
+	int cutoff;
 	
 	int readFasta();
 	int readNames();
 	int processList(ListVector*&);
 	string getConsSeq(string, ofstream&, string&, int);
-	char getBase(vector<int>);
+	char getBase(vector<int>, int);
 };
 
 #endif