Represents a SAM sequence entry. More...

#include <SamSequence.h>

Public Member Functions
	SamSequence ()
	default constructor More...

	SamSequence (const std::string &name, const int &length)
	constructs sequence with name and length More...

	SamSequence (const std::string &name, const std::string &length)
	constructs sequence with name and length More...

void	Clear ()
	Clears all data fields. More...

bool	HasAssemblyID () const
	Returns `true` if sequence contains @SQ AS:<AssemblyID> More...

bool	HasChecksum () const
	Returns `true` if sequence contains @SQ M5:<Checksum> More...

bool	HasLength () const
	Returns `true` if sequence contains @SQ LN:<Length> More...

bool	HasName () const
	Returns `true` if sequence contains @SQ SN:<Name> More...

bool	HasSpecies () const
	Returns `true` if sequence contains @SQ SP:<Species> More...

bool	HasURI () const
	Returns `true` if sequence contains @SQ UR:<URI> More...

Public Attributes
std::string	AssemblyID
	corresponds to @SQ AS:<AssemblyID> More...

std::string	Checksum
	corresponds to @SQ M5:<Checksum> More...

std::string	Length
	corresponds to @SQ LN:<Length> More...

std::string	Name
	corresponds to @SQ SN:<Name> More...

std::string	Species
	corresponds to @SQ SP:<Species> More...

std::string	URI
	corresponds to @SQ UR:<URI> More...

std::vector< CustomHeaderTag >	CustomTags

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() [1/3]

SamSequence::SamSequence ( )

default constructor

◆ SamSequence() [2/3]

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() [3/3]

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)

Member Function Documentation

◆ Clear()

void SamSequence::Clear ( )

Clears all data fields.

◆ HasAssemblyID()

bool SamSequence::HasAssemblyID ( ) const

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

◆ HasChecksum()

bool SamSequence::HasChecksum ( ) const

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

◆ HasLength()

bool SamSequence::HasLength ( ) const

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

◆ HasName()

bool SamSequence::HasName ( ) const

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

◆ HasSpecies()

bool SamSequence::HasSpecies ( ) const

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

◆ HasURI()

bool SamSequence::HasURI ( ) const

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

Member Data Documentation

◆ AssemblyID

SamSequence::AssemblyID

corresponds to @SQ AS:<AssemblyID>

◆ Checksum

SamSequence::Checksum

corresponds to @SQ M5:<Checksum>

◆ CustomTags

std::vector<CustomHeaderTag> BamTools::SamSequence::CustomTags

◆ Length

SamSequence::Length

corresponds to @SQ LN:<Length>

Required for valid SAM header.

◆ Name

SamSequence::Name

corresponds to @SQ SN:<Name>