streaming-pileupy

================= Streaming Pileupy

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Create multi-sample text-pileups of streaming SAM/BAM files.

• Free software: MIT license
• Documentation: https://streaming-pileupy.readthedocs.io.

Features

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


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History
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0.5.0 (2020-05-05)
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* Add base quality filter (-Q)

0.4.0 (2020-05-05)
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* Add support for python 3.6

0.3.0 (2020-05-05)
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* Add support for basic pileup functionality

0.2.1 (2020-05-04)
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* First release on PyPI.