fixes while testing 1.33.0

[mothur.git] / parsefastaqcommand.h

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index c45405f42455de7bbdf93d7f2c391756d0700a05..2ac141626b4b528d352d2860dc64e65826e22357 100644 (file)
--- 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