X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensusseqscommand.h;h=1459b43d25bd54b525459721b5de55a5a1d6d9f6;hb=0cefb55a2616975bd4a144fc345693695ffc9bb6;hp=226b4c959bf25f9c0629a556755641809401baa4;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git diff --git a/consensusseqscommand.h b/consensusseqscommand.h index 226b4c9..1459b43 100644 --- a/consensusseqscommand.h +++ b/consensusseqscommand.h @@ -1,6 +1,6 @@ #ifndef CONSENSUSSEQSCOMMAND_H #define CONSENSUSSEQSCOMMAND_H - +//test /* * consensusseqscommand.h * Mothur @@ -23,8 +23,11 @@ public: vector setParameters(); string getCommandName() { return "consensus.seqs"; } string getCommandCategory() { return "Sequence Processing"; } + string getOutputFileNameTag(string, string); 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 +41,13 @@ private: map fastaMap; map nameMap; map nameFileMap; + int cutoff; int readFasta(); int readNames(); int processList(ListVector*&); string getConsSeq(string, ofstream&, string&, int); - char getBase(vector); + char getBase(vector, int); }; #endif