X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcrseqscommand.h;h=9fc40419411ff2535f01eb150699b30227225a3b;hb=4b54ce99af7db8019ea907cd7c2edf789369ada9;hp=45ce6f3f153e6020f00c859b1928cc1d74ea2a55;hpb=bb8d942036365d2a66330944269f17841ed2388a;p=mothur.git diff --git a/pcrseqscommand.h b/pcrseqscommand.h index 45ce6f3..9fc4041 100644 --- a/pcrseqscommand.h +++ b/pcrseqscommand.h @@ -15,6 +15,7 @@ #include "trimoligos.h" #include "alignment.hpp" #include "needlemanoverlap.hpp" +#include "counttable.h" class PcrSeqsCommand : public Command { public: @@ -25,7 +26,9 @@ public: vector setParameters(); string getCommandName() { return "pcr.seqs"; } string getCommandCategory() { return "Sequence Processing"; } + string getHelpString(); + string getOutputPattern(string); string getCitation() { return "http://www.mothur.org/wiki/Pcr.seqs"; } string getDescription() { return "pcr.seqs"; } @@ -44,8 +47,8 @@ private: vector lines; bool getOligos(vector >&, vector >&, vector >&); bool abort, keepprimer, keepdots; - string fastafile, oligosfile, taxfile, groupfile, namefile, ecolifile, outputDir, nomatch; - int start, end, pdiffs, processors, length; + string fastafile, oligosfile, taxfile, groupfile, namefile, countfile, ecolifile, outputDir, nomatch; + int start, end, processors, length; vector revPrimer, outputNames; vector primers; @@ -54,6 +57,7 @@ private: int readName(set&); int readGroup(set); int readTax(set); + int readCount(set); bool readOligos(); bool readEcoli(); int driverPcr(string, string, string, set&, linePair);