BamTools::SamSequence Struct Reference

Represents a SAM sequence entry. More...

#include <SamSequence.h>

List of all members.

Public Member Functions
	SamSequence (void)
	default constructor
	SamSequence (const std::string &name, const int &length)
	constructs sequence with name and length
	SamSequence (const std::string &name, const std::string &length)
	constructs sequence with name and length
	SamSequence (const SamSequence &other)
	copy constructor
	~SamSequence (void)
	destructor
void	Clear (void)
	Clears all data fields.
bool	HasAssemblyID (void) const
	Returns true if sequence contains @SQ AS:<AssemblyID>
bool	HasChecksum (void) const
	Returns true if sequence contains @SQ M5:<Checksum>
bool	HasLength (void) const
	Returns true if sequence contains @SQ LN:<Length>
bool	HasName (void) const
	Returns true if sequence contains @SQ SN:<Name>
bool	HasSpecies (void) const
	Returns true if sequence contains @SQ SP:<Species>
bool	HasURI (void) const
	Returns true if sequence contains @SQ UR:<URI>
Public Attributes
std::string	AssemblyID
	corresponds to @SQ AS:<AssemblyID>
std::string	Checksum
	corresponds to @SQ M5:<Checksum>
std::string	Length
	corresponds to @SQ LN:<Length>
std::string	Name
	corresponds to @SQ SN:<Name>
std::string	Species
	corresponds to @SQ SP:<Species>
std::string	URI
	corresponds to @SQ UR:<URI>

---

Detailed Description

Represents a SAM sequence entry.

Provides direct read/write access to the SAM sequence data fields.

See also:

http://samtools.sourceforge.net/SAM1.pdf

---

Constructor & Destructor Documentation

SamSequence::SamSequence

(

void

)

default constructor

SamSequence::SamSequence	(	const std::string &	name,
		const int &	length
	)

constructs sequence with name and length

Parameters:

	name	desired sequence name
	length	desired sequence length (numeric value)

SamSequence::SamSequence	(	const std::string &	name,
		const std::string &	length
	)

constructs sequence with name and length

Parameters:

	name	desired sequence name
	length	desired sequence length (string value)

SamSequence::SamSequence

(

const SamSequence &

other

)

copy constructor

SamSequence::~SamSequence

(

void

)

destructor

---

Member Function Documentation

void SamSequence::Clear

(

void

)

Clears all data fields.

bool SamSequence::HasAssemblyID

(

void

)

const

Returns true if sequence contains @SQ AS:<AssemblyID>

bool SamSequence::HasChecksum

(

void

)

const

Returns true if sequence contains @SQ M5:<Checksum>

bool SamSequence::HasLength

(

void

)

const

Returns true if sequence contains @SQ LN:<Length>

bool SamSequence::HasName

(

void

)

const

Returns true if sequence contains @SQ SN:<Name>

bool SamSequence::HasSpecies

(

void

)

const

Returns true if sequence contains @SQ SP:<Species>

bool SamSequence::HasURI

(

void

)

const

Returns true if sequence contains @SQ UR:<URI>

---

Member Data Documentation

SamSequence::AssemblyID

corresponds to @SQ AS:<AssemblyID>

SamSequence::Checksum

corresponds to @SQ M5:<Checksum>

SamSequence::Length

corresponds to @SQ LN:<Length>

Required for valid SAM header.

SamSequence::Name

corresponds to @SQ SN:<Name>

Required for valid SAM header.

SamSequence::Species

corresponds to @SQ SP:<Species>

SamSequence::URI

corresponds to @SQ UR:<URI>

---

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

• SamSequence.h
• SamSequence.cpp