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README.md

1# pbbam
2
3[![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)
4
5As of the 3.0 release of SMRTanalysis, PacBio is embracing the industry standard BAM
6format for (both aligned and unaligned) basecall data files. We have also formulated
7a BAM companion file format (bam.pbi) enabling fast access to a richer set of per-read
8information as well as compatibility for software built around the legacy cmp.h5 format.
9
10The **pbbam** software package provides components to create, query, & edit PacBio BAM
11files and associated indices. These components include a core C++ library, bindings for
12additional languages, and command-line utilities.
13
14### Note:
15
16This 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.
17
18##  Documentation
19
20  - [Documentation Home](http://pbbam.readthedocs.org/en/latest/index.html)
21    - [Getting Started](http://pbbam.readthedocs.org/en/latest/getting_started.html)
22    - [C++ API Reference](http://pbbam.readthedocs.org/en/latest/api_reference.html)
23
24  - [Changelog](https://github.com/PacificBiosciences/pbbam/blob/master/CHANGELOG.md)
25
26## FAQ
27
28### [Help! I am getting "unsupported sequencing chemistry combination"!](#chemistry-bundle)
29
30**pbbam** validates all BAM files, and as part of this validation, it checks whether the
31`BindingKit` and `SequencingKit` variables in every ReadGroup of the provided BAM file are
32known. As part of ongoing chemistry developments, we might need to introduce new part numbers
33to identify novel reagents and/or SMRT Cells. You are unlikely to encounter such issues
34when using SMRT Link, as it has an integrated auto-updater that will periodically check and
35install new chemistries automatically. All PacBio tools being used without a proper SMRT Link
36installation will require manual intervention to download new chemistries:
37
38  ```sh
39  cd <some persistent dir>
40  export SMRT_CHEMISTRY_BUNDLE_DIR="${PWD}"
41
42  wget https://raw.githubusercontent.com/PacificBiosciences/pbcore/develop/pbcore/chemistry/resources/mapping.xml -O chemistry.xml
43  ```
44
45This will cause **pbbam** to try to load the out-of-band `chemistry.xml` from
46`SMRT_CHEMISTRY_BUNDLE_DIR` and should allow you to use somewhat older software
47with somewhat newer BAMs. **Note:** this only allows **pbbam**'s internal validation
48to pass, this will not automatically make other chemistry-dependent software work
49with newer chemistries. For instance, Arrow's backend ([Unanimity](https://github.com/PacificBiosciences/unanimity))
50is parametrized on chemistry too, and it will fail should a completely new chemistry
51be introduced. See Unanimity's FAQ on how to employ `SMRT_CHEMISTRY_BUNDLE_DIR`
52to load models for new chemistries.
53
54
55## License
56
57 - [PacBio open source license](https://github.com/PacificBiosciences/pbbam/blob/master/LICENSE.txt)
58
59DISCLAIMER
60----------
61THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.
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