BamTools  2.4.0
Public Member Functions | Public Attributes | List of all members
BamTools::SamSequence Struct Reference

Represents a SAM sequence entry. More...

#include <SamSequence.h>

Public Member Functions

 SamSequence (void)
 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...
 
 SamSequence (const SamSequence &other)
 copy constructor More...
 
 ~SamSequence (void)
 destructor More...
 
void Clear (void)
 Clears all data fields. More...
 
bool HasAssemblyID (void) const
 Returns true if sequence contains @SQ AS:<AssemblyID> More...
 
bool HasChecksum (void) const
 Returns true if sequence contains @SQ M5:<Checksum> More...
 
bool HasLength (void) const
 Returns true if sequence contains @SQ LN:<Length> More...
 
bool HasName (void) const
 Returns true if sequence contains @SQ SN:<Name> More...
 
bool HasSpecies (void) const
 Returns true if sequence contains @SQ SP:<Species> More...
 
bool HasURI (void) 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< 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::SamSequence ( void  )

default constructor

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

constructs sequence with name and length

Parameters
namedesired sequence name
lengthdesired 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>

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