X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcrseqscommand.h;h=9fc40419411ff2535f01eb150699b30227225a3b;hb=20071b183e619c122bf9f63b4bb42722507c4e4a;hp=baeca4eedc66ac9aa38acaa4b7d65bfebca56410;hpb=f687723a8357916e86a05116978e6869b039ce36;p=mothur.git

diff --git a/pcrseqscommand.h b/pcrseqscommand.h
index baeca4e..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:
@@ -25,8 +26,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "pcr.seqs";	}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Pcr.seqs"; }
 	string getDescription()		{ return "pcr.seqs"; }
     
@@ -45,7 +47,7 @@ private:
     vector<linePair> lines;
 	bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
     bool abort, keepprimer, keepdots;
-	string fastafile, oligosfile, taxfile, groupfile, namefile, ecolifile, outputDir, nomatch;
+	string fastafile, oligosfile, taxfile, groupfile, namefile, countfile, ecolifile, outputDir, nomatch;
 	int start, end, processors, length;
 	
     vector<string> revPrimer, outputNames;
@@ -55,6 +57,7 @@ private:
     int readName(set<string>&);
     int readGroup(set<string>);
     int readTax(set<string>);
+    int readCount(set<string>);
     bool readOligos();
     bool readEcoli();
 	int driverPcr(string, string, string, set<string>&, linePair);