vdj_pipe::Parser_fastq Class Reference

Parser for FASTQ files. More...

#include <parser_fastq.hpp>

Inheritance diagram for vdj_pipe::Parser_fastq:

Collaboration diagram for vdj_pipe::Parser_fastq:

Public Types
typedef Seq_qual_record	record
typedef record::sequence	sequence
typedef record::quality	quality

Public Member Functions
	Parser_fastq (File_input const &fi, const char offset=qual_offset)
	Parser_fastq (std::istream &is, const compression::Compression compr=compression::none, const char offset=qual_offset)
void	next_record ()
const boost::string_ref	get_id ()
const boost::string_ref	get_defstr ()
sequence	get_sequence ()
quality	get_qual ()
template<class InsertIter >
void	get_qual (InsertIter i)
record	get_record ()
Public Member Functions inherited from vdj_pipe::detail::Parser_line
int	line_num () const
bool	has_next () const

Static Public Attributes
static const char	qual_offset = -33

Private Types
enum	State { Def, Seq, Qual, End }

Private Attributes
const char	offset_
State	state_

Additional Inherited Members
Protected Member Functions inherited from vdj_pipe::detail::Parser_line
	Parser_line (File_input const &fi)
	Parser_line (std::istream &is, const compression::Compression compr)
void	skip_line ()
void	seek_line (const char tag)
const boost::string_ref	get_id (const char tag)
void	set_meta (Seq_meta &sm, const char tag)
const boost::string_ref	get_defstr (const char tag)
std::string	get_sequence (const char tag)
void	check () const
Protected Attributes inherited from vdj_pipe::detail::Parser_line
File_istream	fis_
std::string	str_
int	line_

Detailed Description

Parser for FASTQ files.

Read, possibly compressed, FASTQ files

Member Typedef Documentation

typedef record::quality vdj_pipe::Parser_fastq::quality

typedef Seq_qual_record vdj_pipe::Parser_fastq::record

typedef record::sequence vdj_pipe::Parser_fastq::sequence

Member Enumeration Documentation

enum vdj_pipe::Parser_fastq::State

private

Enumerator
Def
Seq
Qual
End

Constructor & Destructor Documentation

vdj_pipe::Parser_fastq::Parser_fastq ( File_input const &  fi, const char  offset = qual_offset  )

inlineexplicit

vdj_pipe::Parser_fastq::Parser_fastq ( std::istream &  is, const compression::Compression  compr = compression::none, const char  offset = qual_offset  )

inlineexplicit

Member Function Documentation

const boost::string_ref vdj_pipe::Parser_fastq::get_defstr ( )

inline

const boost::string_ref vdj_pipe::Parser_fastq::get_id ( )

inline

quality vdj_pipe::Parser_fastq::get_qual ( )

inline

template<class InsertIter >

void vdj_pipe::Parser_fastq::get_qual ( InsertIter  i )

inline

record vdj_pipe::Parser_fastq::get_record ( )

inline

sequence vdj_pipe::Parser_fastq::get_sequence ( )

inline

void vdj_pipe::Parser_fastq::next_record ( )

inline

Member Data Documentation

const char vdj_pipe::Parser_fastq::offset_

private

const char vdj_pipe::Parser_fastq::qual_offset = -33

static

State vdj_pipe::Parser_fastq::state_

private

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The documentation for this class was generated from the following file:

• include/vdj_pipe/parser_fastq.hpp