Metadata-Version: 1.2
Name: streaming_pileupy
Version: 0.5.7
Summary: Create multi-sample text-pileups of streaming SAM/BAM files.
Home-page: https://github.com/winni2k/streaming_pileupy
Author: Warren W. Kretzschmar
Author-email: winni@warrenwk.com
License: MIT license
Description: =================
        Streaming Pileupy
        =================
        
        
        .. 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.
        
        
        * 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
        
        
        =======
        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.
        
Keywords: streaming_pileupy
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
