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(const PbiIndex &other)
PbiIndex(PbiIndex&&)
PbiIndex &operator=(const PbiIndex &other)
PbiIndex &operator=(PbiIndex&&)
~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