PbiIndex¶
#include <pbbam/PbiIndex.h>
-
class
PacBio::BAM::
PbiIndex
¶ The PbiIndex class provides an representation of PBI index data that is rearranged for quick lookups.
The PbiIndex class itself provides access to a few high-level attributes (e.g. version, number of records, etc.). The actual lookup data is stored in its member components: BasicLookupData, MappedLookupData, ReferenceLookupData, & BarcodeLookupData .
Constructors & Related Methods
-
PbiIndex
(const std::string &pbiFilename)¶ Creates a PbiIndex lookup structure from a PBI file.
- Parameters
pbiFilename
: filename
- Exceptions
std::runtime_error
: if failed to load data from file
-
~PbiIndex
()¶
PBI General Attributes
-
bool
HasBarcodeData
() const¶ - Return
- true if index has BarcodeData section
-
bool
HasMappedData
() const¶ - Return
- true if index has MappedData section
-
bool
HasReferenceData
() const¶ - Return
- true if index has ReferenceData section
-
bool
HasSection
(const PbiFile::Section section) const¶ - Return
- true if index has section
- Parameters
section
: PbiFile::Section identifier
-
std::string
Filename
() const¶ - Return
- index filename (“*.pbi”)
- Note
- Returns an empty string if the underlying data was generated, not loaded from file.
-
PbiFile::Sections
FileSections
() const¶ - Return
- enum flags representing the file sections present
-
uint32_t
NumReads
() const¶ - Return
- the number of records in the PBI (& associated BAM)
-
PbiFile::VersionEnum
Version
() const¶ - Return
- the PBI file’s version
Lookup Data Components
-
const BarcodeLookupData &
BarcodeData
() const¶ May be empty, check result of HasBarcodeData.
- Return
- const reference to BarcodeData lookup structure
-
const BasicLookupData &
BasicData
() const¶ - Return
- const reference to BasicData lookup structure
-
const MappedLookupData &
MappedData
() const¶ May be empty, check result of HasMappedData.
- Return
- const reference to MappedData lookup structure
-
const ReferenceLookupData &
ReferenceData
() const¶ May be empty, check result of HasReferenceData.
- Return
- const reference to reference data lookup structure
-