X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsefastaqcommand.h;h=2ac141626b4b528d352d2860dc64e65826e22357;hp=c45405f42455de7bbdf93d7f2c391756d0700a05;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index c45405f..2ac1416 100644
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -12,28 +12,66 @@
 
 
 #include "command.hpp"
+#include "trimoligos.h"
+#include "sequence.hpp"
+#include "groupmap.h"
+
+struct fastqRead2 {
+    string quality;
+	Sequence seq;
+    string wholeRead;
+	
+	fastqRead2() {  };
+	fastqRead2(Sequence s, string q, string w) : seq(s), quality(q), wholeRead(w){};
+	~fastqRead2() {};
+};
+
 
 class ParseFastaQCommand : public Command {
 
 public:
 	ParseFastaQCommand(string);
 	ParseFastaQCommand();
-	~ParseFastaQCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();	
+	~ParseFastaQCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "fastq.info";		}
+	string getCommandCategory()		{ return "Sequence Processing"; }
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
+	string getDescription()		{ return "reads a fastq file and creates a fasta and quality file"; }
+
 	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }		
 private:
 
 	vector<string> outputNames;	
-	map<string, vector<string> > outputTypes;
-	string outputDir, fastaQFile;
-	bool abort;
+	string outputDir, fastaQFile, format, oligosfile, groupfile;
+	bool abort, fasta, qual, pacbio, pairedOligos;
+    int pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, split;
+    GroupMap* groupMap;
+    
+    //oligos file data structures
+    vector<string> linker, spacer, primerNameVector, barcodeNameVector, revPrimer;
+	map<string, int> barcodes;
+	map<string, int> primers;
+    map<int, oligosPair> pairedBarcodes;
+    map<int, oligosPair> pairedPrimers;
+    vector<vector<string> > fastqFileNames;
+    string noMatchFile;
 	
 	vector<int> convertQual(string);
+    vector<char> convertTable;
+    bool readOligos(string oligosFile);
+    bool readGroup(string oligosFile);
+    string reverseOligo(string oligo);
+    fastqRead2 readFastq(ifstream&, bool&);
+    int findGroup(fastqRead2, int&, int&, TrimOligos*&, int, int);
+    int findGroup(fastqRead2, int&, int&, string);
+    
 };
 
 #endif