X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsefastaqcommand.h;h=2ac141626b4b528d352d2860dc64e65826e22357;hp=5ae6b9c482fe6b4022bb4d4c5d4ae2e79ea3aad8;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=e9845ee4c8db2e044e87d721cc2d94f8d609e03d

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index 5ae6b9c..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 {
 
@@ -35,11 +49,29 @@ public:
 private:
 
 	vector<string> outputNames;	
-	string outputDir, fastaQFile, format;
-	bool abort, fasta, qual, pacbio;
+	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