Short read data type. More...

Classes
struct	accessory
	Additional read information, usually represented as optional tags. More...

Public Types
enum	InsertState { PE_UNSPECIFIED, PE_FILTER_ORPHAN, PE_TECHNICAL, PE_PAIRED }
	Paired end sequencing attributes. More...

enum	PeOrientation { ORI_UNSPECIFIED, ORI_TOWARDS, ORI_AWAY, ORI_SAME }
	Expected orientation relative to read1. More...

typedef bool(*	compare_type )(const read &, const read &)

Public Member Functions
	read ()
	Constructor, init defaults.

bool	is_firstread () const
	First read of a PE or single end run.

bool	is_lastread () const
	Second read of a PE run.

int	get_qual_std (const size_t pos) const
	Get integer quality value for a position.

void	get_part (shore::read &buf, size_t left, size_t right, bool set_tags) const
	Get the part of the read between left and right. More...

void	get_clipped_read (shore::read &buf, bool set_tags=false) const
	Get the part of the read between CLL and CLR. More...

void	get_read_prefix (shore::read &buf, bool set_tags=false) const
	Get the part of the read that comes before CLL. More...

void	get_read_suffix (shore::read &buf, bool set_tags=false) const
	Get the part of the read that follows CLR. More...

Static Public Member Functions
static bool	cmp_id (const read &r1, const read &r2)
	ID comparator.

static bool	cmp_seq (const read &r1, const read &r2)
	Sequence comparator.

static bool	cmp_id_str (const std::string &id1, const std::string &id2)
	ID comparator (string version).

static void	qual_sanger2illumina (std::string &qual)
	Convert a quality string from sanger format to solexa/illumina 1.3+ format.

static void	qual_illumina2sanger (std::string &qual)
	Convert a quality string from solexa/illumina 1.3+ format to sanger format.

static void	qual_solexa2sanger (std::string &qual)
	Convert a quality string from solexa/illumina 1.0 format to sanger format.

static char	enc_qual_sanger (const int q)
	Convert an integer quality value to sanger char encoding.

static int	dec_qual_sanger (const char q)
	Convert a quality value in sanger char encoding tpo integer.

Public Attributes
std::string	id
	ID of the fragment that the read comes from.

std::string	sequence
	Sequence of the read.

std::string	qual_std
	Quality string.

int	index
	Index of this read. More...

InsertState	pe_state

std::string	qual_aux
	Auxiliary quality string.

accessory	tags
	Optional information, e.g. filtering.

Static Public Attributes
static const int	ASCIIENC_ILLUMINA =64
	ASCII offset for quality zero in illumina encoding.

static const int	ASCIIENC_SANGER =33
	ASCII offset for quality zero in sanger encoding.

static const int	ASCIIENC_CHASTITY =-10
	ASCII offset for chastity 50.

static const char	insstate_enc [5]

static const char *	ori_conv [4]

Detailed Description

Short read data type.

Member Enumeration Documentation

Paired end sequencing attributes.

Enumerator
PE_UNSPECIFIED	Any of the below.
PE_FILTER_ORPHAN	Partner lost due to quality filtering.
PE_TECHNICAL	E.g. barcode read.
PE_PAIRED	Not PE_FILTER_ORPHAN or PE_TECHNICAL.

Expected orientation relative to read1.

void shore::read::get_clipped_read	(	shore::read &	buf,
		bool	set_tags = `false`
	)		const

Get the part of the read between CLL and CLR.

Parameters

set_tags Also copy the tag values (except CLL / CLR).

Get the part of the read between left and right.

Parameters

set_tags Also copy the tag values (except CLL / CLR).

void shore::read::get_read_prefix	(	shore::read &	buf,
		bool	set_tags = `false`
	)		const

Get the part of the read that comes before CLL.

Parameters

set_tags Also copy the tag values (except CLL / CLR).

void shore::read::get_read_suffix	(	shore::read &	buf,
		bool	set_tags = `false`
	)		const

Get the part of the read that follows CLR.

Parameters

set_tags Also copy the tag values (except CLL / CLR).

int shore::read::index

Index of this read.

0: unpaired read 1..n: paired end or other multi-part read

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