BamTools 2.5.2
|
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< CustomHeaderTag > | CustomTags |
Represents a SAM sequence entry.
Provides direct read/write access to the SAM sequence data fields.
SamSequence::SamSequence | ( | ) |
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) |
void SamSequence::Clear | ( | ) |
Clears all data fields.
bool SamSequence::HasAssemblyID | ( | ) | const |
Returns true
if sequence contains @SQ AS:<AssemblyID>
bool SamSequence::HasChecksum | ( | ) | const |
Returns true
if sequence contains @SQ M5:<Checksum>
bool SamSequence::HasLength | ( | ) | const |
Returns true
if sequence contains @SQ LN:<Length>
bool SamSequence::HasName | ( | ) | const |
Returns true
if sequence contains @SQ SN:<Name>
bool SamSequence::HasSpecies | ( | ) | const |
Returns true
if sequence contains @SQ SP:<Species>
bool SamSequence::HasURI | ( | ) | 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>