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README.rst
1===== 2Pysam 3===== 4 5|build-status| |docs| 6 7Pysam is a python module for reading and manipulating files in the 8SAM/BAM format. The SAM/BAM format is a way to store efficiently large 9numbers of alignments (`Li 2009`_), such as those routinely created by 10next-generation sequencing methods. 11 12Pysam is a lightweight wrapper of the samtools_ C-API. Pysam also 13includes an interface for tabix_. 14 15If you are using the conda packaging manager (e.g. miniconda or anaconda), 16you can install pysam from the `bioconda channel <https://bioconda.github.io/>`_:: 17 18 conda config --add channels defaults 19 conda config --add channels conda-forge 20 conda config --add channels bioconda 21 conda install pysam 22 23Installation through bioconda is the recommended way to install pysam 24as it resolves non-python dependencies and uses pre-configured 25compilation options. Especially for OS X this will potentially save a 26lot of trouble. 27 28The current version of pysam wraps 3rd-party code from htslib-1.14, samtools-1.14, and bcftools-1.14. 29 30Pysam is available through `pypi 31<https://pypi.python.org/pypi/pysam>`_. To install, type:: 32 33 pip install pysam 34 35Pysam documentation is available 36`here <http://pysam.readthedocs.org/en/latest/>`_ 37 38Questions and comments are very welcome and should be sent to the 39`pysam user group <http://groups.google.com/group/pysam-user-group>`_ 40 41.. _samtools: http://samtools.sourceforge.net/ 42.. _tabix: http://samtools.sourceforge.net/tabix.shtml 43.. _Li 2009: http://www.ncbi.nlm.nih.gov/pubmed/19505943 44 45.. |build-status| image:: https://travis-ci.org/pysam-developers/pysam.svg 46 :alt: build status 47 :scale: 100% 48 :target: https://travis-ci.org/pysam-developers/pysam 49 50.. |docs| image:: https://readthedocs.org/projects/pysam/badge/?version=latest 51 :alt: Documentation Status 52 :scale: 100% 53 :target: https://pysam.readthedocs.org/en/latest/?badge=latest 54