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# pbbam

[![Build Status](https://travis-ci.org/PacificBiosciences/pbbam.svg?branch=master)](https://travis-ci.org/PacificBiosciences/pbbam) [![Documentation Status](https://readthedocs.org/projects/pbbam/badge/?version=latest)](http://pbbam.readthedocs.org/en/latest/?badge=latest)
 
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.

### Note:

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](https://github.com/PacificBiosciences/PacBioFileFormats/blob/3.0/BAM.rst). Non-PacBio BAMs will cause exceptions to be thrown.
 
##  Documentation

  - [Documentation Home](http://pbbam.readthedocs.org/en/latest/index.html)
    - [Getting Started](http://pbbam.readthedocs.org/en/latest/getting_started.html)
    - [C++ API Reference](http://pbbam.readthedocs.org/en/latest/api_reference.html)

  - [Changelog](https://github.com/PacificBiosciences/pbbam/blob/master/CHANGELOG.md)

## License

 - [PacBio open source license](https://github.com/PacificBiosciences/pbbam/blob/master/LICENSE.txt)