PbiRawData

#include <pbbam/PbiRawData.h>
class PacBio::BAM::PbiRawData

The PbiRawData class provides an representation of raw PBI index data, used mostly for construction or I/O.

The PbiRawData class itself provides access to a few high-level attributes (e.g. version, number of records, etc.). The actual index data is stored in its member components: PbiRawBasicData, PbiRawMappedData, PbiRawReferenceData, & PbiRawBarcodeData .

Constructors & Related Methods

PbiRawData()

Creates an empty raw data structure, ready for building.

PbiRawData(const std::string &pbiFilename)

Loads raw PBI data from a file.

Parameters
  • pbiFilename: ”.pbi” filename
Exceptions
  • std::runtime_error: if file contents cannot be loaded properly

PbiRawData(const DataSet &dataset)

Loads a raw, aggregate PBI data from a dataset.

This constructor creates a raw index object that contains an aggregation of index data across the dataset.

Note
ReferenceData (the per-reference table for coordinate-sorted data) is not currently available for the index aggregate. All other per-record data sections will be present.
Parameters
Exceptions
  • std::runtime_error: if file(s) contents cannot be loaded properly

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

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 calculated in code or aggregated from a DataSet, rather than loaded from a single PBI 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(s)

PbiFile::VersionEnum Version() const

Return
the PBI file’s version

PbiRawData &FileSections(PbiFile::Sections sections)

Sets the file section flags.

Return
reference to this index
Parameters
  • sections: section flags

PbiRawData &NumReads(uint32_t num)

Sets the number of indexed records.

Return
reference to this index
Parameters
  • num: number of records

PbiRawData &Version(PbiFile::VersionEnum version)

Sets PBI file version.

Return
reference to this index
Parameters
  • version: file version

Raw Data Components

const PbiRawBarcodeData &BarcodeData() const

May be empty, check result of HasBarcodeData.

Return
const reference to BarcodeData lookup structure

const PbiRawBasicData &BasicData() const

Return
const reference to BasicData lookup structure

const PbiRawMappedData &MappedData() const

May be empty, check result of HasMappedData.

Return
const reference to MappedData lookup structure

const PbiRawReferenceData &ReferenceData() const

May be empty, check result of HasReferenceData.

Return
const reference to reference data lookup structure

PbiRawBarcodeData &BarcodeData()

May be empty, check result of HasBarcodeData.

Return
reference to BarcodeData lookup structure

PbiRawBasicData &BasicData()

Return
reference to BasicData lookup structure

PbiRawMappedData &MappedData()

May be empty, check result of HasMappedData.

Return
reference to MappedData lookup structure

PbiRawReferenceData &ReferenceData()

May be empty, check result of HasReferenceData.

Return
reference to reference data lookup structure