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

The GenomicIntervalCompositeBamReader class provides read access to multipe BAM files, limiting results to a genomic region.

Requires a ”.bai” file for each input BAM file.

Results will be returned in order of genomic coordinate (first by reference ID, then by position).

Contstructors & Related Methods

GenomicIntervalCompositeBamReader(const GenomicInterval &interval, const std::vector<BamFile> &bamFiles)
GenomicIntervalCompositeBamReader(const GenomicInterval &interval, std::vector<BamFile> &&bamFiles)
GenomicIntervalCompositeBamReader(const GenomicInterval &interval, const DataSet &dataset)

Data Access

bool GetNext(BamRecord &record)

Fetches next BAM record in the interval specified, storing in record

true on success, false if no more data available.
  • record:

GenomicIntervalCompositeBamReader &Interval(const GenomicInterval &interval)

Sets a new genomic interval of interest.

reference to this reader

const GenomicInterval &Interval() const

the current specified interval