PbiRawMappedData

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

The PbiRawMappedData class represents the raw data stored in the “MappedData” section of the PBI index.

Constructors & Related Methods

PbiRawMappedData()

Creates an empty data structure.

PbiRawMappedData(uint32_t numReads)

Creates an empty data structure, preallocating space for a known number of records.

PbiRawMappedData(const PbiRawMappedData &other)
PbiRawMappedData(PbiRawMappedData &&other)
PbiRawMappedData &operator=(const PbiRawMappedData &other)
PbiRawMappedData &operator=(PbiRawMappedData &&other)

Index Construction

void AddRecord(const BamRecord &b)

Adds a record’s mapping data.

Parameters
  • b: BAM record

Index Data Query

uint32_t NumDeletedBasesAt(size_t recordIndex) const

Calculates the number of deleted bases for a particular record.

Convenvience method. Equivalent to: 

NumDeletedAndInsertedBasesAt(i).first;

Return
number of deleted bases
Parameters
  • recordIndex: i-th record

uint32_t NumInsertedBasesAt(size_t recordIndex) const

Calculates the number of inserted bases for a particular record.

Convenvience method. Equivalent to: 

NumDeletedAndInsertedBasesAt(i).second;

Return
number of inserted bases
Parameters
  • recordIndex: i-th record

std::pair<uint32_t, uint32_t> NumDeletedAndInsertedBasesAt(size_t recordIndex) const

Calculates the number of deleted & inserted bases for a particular record.

Return
a pair consisting of (numDeletions,numInsertions)
Parameters
  • recordIndex: i-th record in the data set

Raw Data Containers

std::vector<int32_t> tId_
std::vector<uint32_t> tStart_
std::vector<uint32_t> tEnd_
std::vector<uint32_t> aStart_
std::vector<uint32_t> aEnd_
std::vector<uint8_t> revStrand_
std::vector<uint32_t> nM_
std::vector<uint32_t> nMM_
std::vector<uint8_t> mapQV_