Parser for FASTQ files. More...

Inheritance diagram for vdj_pipe::Parser_fastq:

Collaboration diagram for vdj_pipe::Parser_fastq:

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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

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

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

Public Types