BamTools 2.5.2
Loading...
Searching...
No Matches
BamTools::SamSequence Struct Reference

Represents a SAM sequence entry. More...

#include <SamSequence.h>

Public Member Functions

 SamSequence ()
 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
 
void Clear ()
 Clears all data fields.
 
bool HasAssemblyID () const
 Returns true if sequence contains @SQ AS:<AssemblyID>
 
bool HasChecksum () const
 Returns true if sequence contains @SQ M5:<Checksum>
 
bool HasLength () const
 Returns true if sequence contains @SQ LN:<Length>
 
bool HasName () const
 Returns true if sequence contains @SQ SN:<Name>
 
bool HasSpecies () const
 Returns true if sequence contains @SQ SP:<Species>
 
bool HasURI () 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>
 
std::vector< CustomHeaderTagCustomTags
 

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
namedesired sequence name
lengthdesired sequence length (numeric value)

◆ SamSequence() [3/3]

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

constructs sequence with name and length

Parameters
namedesired sequence name
lengthdesired 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

std::string BamTools::SamSequence::AssemblyID

corresponds to @SQ AS:<AssemblyID>

◆ Checksum

std::string BamTools::SamSequence::Checksum

corresponds to @SQ M5:<Checksum>

◆ CustomTags

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

◆ Length

std::string BamTools::SamSequence::Length

corresponds to @SQ LN:<Length>

Required for valid SAM header.

◆ Name

std::string BamTools::SamSequence::Name

corresponds to @SQ SN:<Name>

Required for valid SAM header.

◆ Species

std::string BamTools::SamSequence::Species

corresponds to @SQ SP:<Species>

◆ URI

std::string BamTools::SamSequence::URI

corresponds to @SQ UR:<URI>


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