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.. image:: https://img.shields.io/pypi/v/streaming_pileupy.svg :target: https://pypi.python.org/pypi/streaming_pileupy
.. image:: https://img.shields.io/travis/winni2k/streaming_pileupy.svg :target: https://travis-ci.com/winni2k/streaming_pileupy
.. image:: https://readthedocs.org/projects/streaming-pileupy/badge/?version=latest :target: https://streaming-pileupy.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status
.. image:: https://pyup.io/repos/github/winni2k/streaming_pileupy/shield.svg :target: https://pyup.io/repos/github/winni2k/streaming_pileupy/ :alt: Updates
Create multi-sample text-pileups of streaming SAM/BAM files.
Streaming Pileupy creates a pileup of a single SAM/BAM file using the read group SM identifier to split reads by sample:
.. code-block:: bash
# extract sample names from read group SM tag
samtools view -H input.bam \
| grep '^@RG' \
| perl -pne 's/.*SM:(\S+).*/$1/' \
| sort | uniq > sample_names.txt
# create read-group aware pileup
spileup input.bam sample_names.txt
Base quality filtering
Bases with less than a certain quality can be filtered with ``-Q``.
Missing features
----------------
* Read beginning and end annotations in pileup output
* Deletion annotations in pileup output
* Filter output bases on BED file
Credits
-------
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
=======
History
=======
0.5.0 (2020-05-05)
------------------
* Add base quality filter (-Q)
0.4.0 (2020-05-05)
------------------
* Add support for python 3.6
0.3.0 (2020-05-05)
------------------
* Add support for basic pileup functionality
0.2.1 (2020-05-04)
------------------
* First release on PyPI.
FAQs
Create multi-sample text-pileups of streaming SAM/BAM files.
We found that streaming-pileupy demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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