BamTools
2.4.0
|
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< CustomHeaderTag > | CustomTags |
Represents a SAM sequence entry.
Provides direct read/write access to the SAM sequence data fields.
SamSequence::SamSequence | ( | void | ) |
default constructor
SamSequence::SamSequence | ( | const std::string & | name, |
const int & | length | ||
) |
constructs sequence with name and length
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
name | desired sequence name |
length | desired sequence length (string value) |
SamSequence::SamSequence | ( | const SamSequence & | other | ) |
copy constructor
SamSequence::~SamSequence | ( | void | ) |
destructor
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>
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>