gamgee::Fastq Class Reference

Utility class to hold one FastA or FastQ record. More...

#include <fastq.h>

Public Member Functions
	Fastq ()
	creates an empty record More...
	Fastq (std::string name, std::string comment, std::string sequence, std::string quals="")
	creates a full object by assigning all fields More...
	Fastq (const Fastq &)=default
Fastq &	operator= (const Fastq &)=default
	Fastq (Fastq &&)=default
Fastq &	operator= (Fastq &&)=default
bool	operator!= (const Fastq &other) const
	inequality comparison of all fields in the record More...
bool	operator== (const Fastq &other) const
	equality comparison of all fields in the record More...
std::string	name () const
std::string	comment () const
std::string	sequence () const
std::string	quals () const
void	set_name (const std::string &name)
void	set_comment (const std::string &comment)
void	set_sequence (const std::string &sequence)
void	set_quals (const std::string &quals)
void	chop (const int nBases)
	hard clips the first n bases of the read. More...
void	reverse_complement ()
	transform the sequence into it's reverse complement. More...
bool	is_fastq () const
	true if the record has a quals in it's qual field More...

Detailed Description

Utility class to hold one FastA or FastQ record.

Will automatically output a FastA or FastQ based on the presence of quality scores.

Constructor & Destructor Documentation

gamgee::Fastq::Fastq ( )

inline

creates an empty record

gamgee::Fastq::Fastq ( std::string  name, std::string  comment, std::string  sequence, std::string  quals = ""  )

inline

creates a full object by assigning all fields

Parameters

name	sequence name
comment	optional comment
sequence	sequence bases
quals	optional quality scores (leave it out for FastA)

gamgee::Fastq::Fastq ( const Fastq &  )

default

gamgee::Fastq::Fastq ( Fastq &&  )

default

Member Function Documentation

void gamgee::Fastq::chop

(

const int

nBases

)

hard clips the first n bases of the read.

std::string gamgee::Fastq::comment ( ) const

inline

bool gamgee::Fastq::is_fastq

(

)

const

true if the record has a quals in it's qual field

std::string gamgee::Fastq::name ( ) const

inline

bool gamgee::Fastq::operator!= ( const Fastq &  other ) const

inline

inequality comparison of all fields in the record

Returns

true if any field differs (string comparison)

Fastq& gamgee::Fastq::operator= ( const Fastq &  )

default

Fastq& gamgee::Fastq::operator= ( Fastq &&  )

default

bool gamgee::Fastq::operator== ( const Fastq &  other ) const

inline

equality comparison of all fields in the record

Returns

true only if every field is the same (string comparison)

std::string gamgee::Fastq::quals ( ) const

inline

void gamgee::Fastq::reverse_complement

(

)

transform the sequence into it's reverse complement.

std::string gamgee::Fastq::sequence ( ) const

inline

void gamgee::Fastq::set_comment ( const std::string &  comment )

inline

void gamgee::Fastq::set_name ( const std::string &  name )

inline

void gamgee::Fastq::set_quals ( const std::string &  quals )

inline

void gamgee::Fastq::set_sequence ( const std::string &  sequence )

inline

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

• gamgee/fastq.h
• gamgee/fastq.cpp