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//
// filefile.hpp
// Mothur
//
// Created by Sarah Westcott on 12/5/18.
// Copyright © 2018 Schloss Lab. All rights reserved.
//
#ifndef filefile_hpp
#define filefile_hpp
#include "mothurout.h"
#include "utils.hpp"
#include "currentfile.h"
/*
file option 1
sfffile1 oligosfile1
sfffile2 oligosfile2
...
file option 2
fastqfile1 oligosfile1
fastqfile2 oligosfile2
...
file option 3
ffastqfile1 rfastqfile1
ffastqfile2 rfastqfile2
...
file option 4 - only vaild if mode is set to parsefastqpacbio
group1 pacBiofastqfile1
group2 pacBiofastqfile2
...
file option 5
group fastqfile fastqfile
group fastqfile fastqfile
group fastqfile fastqfile
...
file option 6
My.forward.fastq My.reverse.fastq none My.rindex.fastq //none is an option is no forward or reverse index file
...
file option 7 - for make.count command
group fastafile
file option 8 - for make.count command
group forwardFasta reverseFasta
********* fileOption; //1 -> 2 column(4 forms of 2 column), 2 -> 3 column, 3 -> 4 column ******************
*/
/**************************************************************************************************/
class FileFile {
public:
FileFile(string, string); //provide file file and read file, mode (ie. contigs) mode options include: mimarks,contigs,parseFastq,renameSeqs,sra,parsefastqpacbio
~FileFile() = default;
vector< vector<string> > getFiles() { return files; }
bool isColumnWithGroupNames() { return columnWithGroups; }
int getFileFormat() { return fileOption; }
bool isGZ() { return gz; } //are files listed in file compressed
bool containsIndexFiles() { return hasIndex; } //indicates oligos file is required
vector<string> getGroupNames() { return groupNames; } //fileIndex2GroupName, files[0]'s group is -> groupNames[0]
protected:
MothurOut* m;
CurrentFile* current;
Utils util;
string filename, mode, mpath;
bool gz, hasIndex, columnWithGroups;
int fileOption; //1 -> 2 column(3 forms of 2 column), 2 -> 3 column, 3 -> 4 column
vector< vector<string> > files;
vector<string> groupNames;
void read(string, string); //read file, used with () constructor
bool validateFiles(vector<string> pieces, string& forward, string& reverse, string& findex, string& rindex, string& group); //checks locations, abletoOPen, fileOPtion
void setGZ(string forward, string reverse, string findex, string rindex, bool&, bool&);
};
/**************************************************************************************************/
#endif /* filefile_hpp */
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