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.
This library is not intended to be used as a general-purpose BAM utility - all input & output BAMs must adhere to the PacBio BAM format specification. Non-PacBio BAMs will cause exceptions to be thrown.