Metadata-Version: 1.1
Name: vcfpy
Version: 0.3.1
Summary: Python 3 VCF library with good support for both reading and writing
Home-page: https://github.com/bihealth/vcfpy
Author: Manuel Holtgrewe
Author-email: manuel.holtgrewe@bihealth.de
License: MIT license
Description: =====
        VCFPy
        =====
        
        
        .. image:: https://img.shields.io/pypi/v/vcfpy.svg
                :target: https://pypi.python.org/pypi/vcfpy
        
        .. image:: https://img.shields.io/travis/bihealth/vcfpy.svg
                :target: https://travis-ci.org/bihealth/vcfpy
        
        .. image:: https://readthedocs.org/projects/vcfpy/badge/?version=latest
                :target: https://vcfpy.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        .. image:: https://pyup.io/repos/github/bihealth/vcfpy/shield.svg
             :target: https://pyup.io/repos/github/bihealth/vcfpy/
             :alt: Updates
        
        
        Python 3 VCF library with good support for both reading and writing
        
        * Free software: MIT license
        * Documentation: https://vcfpy.readthedocs.io.
        
        
        Features
        --------
        
        - Support for reading and writing VCF v4.3
        - Interface to ``INFO`` and ``FORMAT`` fields is based on ``OrderedDict`` allows for easier modification than PyVCF (also I find this more pythonic)
        - Read (and jump in) and write BGZF files just using ``vcfpy``
        
        Why another VCF parser for Python!
        ----------------------------------
        
        I've been using PyVCF with quite some success in the past.
        However, the main bottleneck of PyVCF is when you want to modify the per-sample genotype information.
        There are some issues in the tracker of PyVCF but none of them can really be considered solved.
        I tried several hours to solve these problems within PyVCF but this never got far or towards a complete rewrite...
        
        For this reason, VCFPy was born and here it is!
        
        What's the State?
        -----------------
        
        VCFPy is the result of two full days of development plus some maintenance work later now (right now).
        I'm using it in several projects but it is not as battle-tested as PyVCF.
        
        Why Python 3 Only?
        ------------------
        
        As I'm only using Python 3 code, I see no advantage in carrying around support for legacy Python 2 and maintaining it.
        At a later point when VCFPy is known to be stable, Python 2 support might be added if someone contributes a pull request.
        
        =======
        History
        =======
        
        HEAD
        ----
        
        0.3.1 (2016-09-21)
        ------------------
        
        * Work around ``FORMAT/FT`` being a string; this is done so in the Delly output
        
        0.3.0 (2016-09-21)
        ------------------
        
        * ``Reader`` and ``Writer`` can now be used as context manager (with ``with``)
        * Including license in documentation, including Biopython license
        * Adding support for writing bgzf files (taken from Biopython)
        * Adding support for parsing arrays in header lines
        * Removing ``example-4.1-bnd.vcf`` example file because v4.1 tumor derival lacks ``ID`` field
        * Adding ``AltAlleleHeaderLine``, ``MetaHeaderLine``, ``PedigreeHeaderLine``, and ``SampleHeaderLine``
        * Renaming ``SimpleHeaderFile`` to ``SimpleHeaderLine``
        * Warn on missing ``FILTER`` entries on parsing
        * Reordered parameters in ``from_stream`` and ``from_file`` (#18)
        * Renamed ``from_file`` to ``from_stream`` (#18)
        * Renamed ``Reader.jump_to`` to ``Reader.fetch``
        * Adding ``header_without_lines`` function
        * Generally extending API to make it esier to use
        * Upgrading dependencies, enabling pyup-bot
        * Greatly extending documentation
        
        0.2.1 (2016-09-19)
        ------------------
        
        * First release on PyPI
        
Keywords: vcfpy
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 :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
