X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsefastaqcommand.h;h=2ac141626b4b528d352d2860dc64e65826e22357;hp=96fcb7d6799358ff4e10f930d1ad4165763b46a0;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=90708fe9701e3827e477c82fb3652539c3bf2a0d

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index 96fcb7d..2ac1416 100644
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -12,6 +12,20 @@
 
 
 #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 {
 
@@ -21,10 +35,11 @@ public:
 	~ParseFastaQCommand() {}
 	
 	vector<string> setParameters();
-	string getCommandName()			{ return "parse.fastq";		}
+	string getCommandName()			{ return "fastq.info";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
-	string getOutputFileNameTag(string, string);
+	
 	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"; }
 
@@ -34,11 +49,29 @@ public:
 private:
 
 	vector<string> outputNames;	
-	string outputDir, fastaQFile, format;
-	bool abort, fasta, qual;
+	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