As of the 3.0 release of SMRTanalysis, PacBio is embracing the industry
standard BAM format for (both aligned and unaligned) basecall data files. We
have also formulated a BAM companion file format (bam.pbi) enabling fast access
to a richer set of per-read information as well as compatibility for software
built around the legacy cmp.h5 format.

The pbbam software package provides components to create, query, & edit PacBio
BAM files and associated indices. These components include a core C++ library,
bindings for additional languages, and command-line utilities.

WWW: https://github.com/PacificBiosciences/pbbam