Metadata-Version: 1.1
Name: jacquard
Version: 0.42
Summary: Command-line tools to expedite analysis of Variant Call Format (VCF) files.
Home-page: https://github.com/umich-brcf-bioinf/Jacquard
Author: University of Michigan Bioinformatics Core
Author-email: bfx-jacquard@umich.edu
License: Apache
Description: ========
        Jacquard
        ========
        Suite of command-line tools to expedite analysis of exome variant data from 
        multiple patients and multiple variant callers.
        
        .. image:: https://travis-ci.org/umich-brcf-bioinf/Jacquard.svg?branch=develop
            :target: https://travis-ci.org/umich-brcf-bioinf/Jacquard
            :alt: Build Status
        
        .. image:: https://coveralls.io/repos/umich-brcf-bioinf/Jacquard/badge.png?branch=develop
            :target: https://coveralls.io/r/umich-brcf-bioinf/Jacquard?branch=develop
            :alt: Coverage Status
        
        .. image:: https://img.shields.io/pypi/l/Jacquard.svg
            :target: https://pypi.python.org/pypi/jacquard/
            :alt: License
        
        .. image:: http://img.shields.io/pypi/v/colour.svg?style=flat
           :target: https://pypi.python.org/pypi/jacquard/
           :alt: Latest PyPI version
        
        .. image:: https://img.shields.io/pypi/dm/Jacquard.svg
           :target: https://pypi.python.org/pypi/jacquard/
            :alt: Downloads Counter
        
        The official repository is at:
        
        https://github.com/umich-brcf-bioinf/Jacquard
        
        Usage
        =====
        
        ::
        
           $ jacquard <subcommand> [options] [arguments]
        
        *Subcommands*
        
        :translate:
           Creates new VCFs, adding a controlled vocabulary of new FORMAT tags.
        :merge:
           Integrates a directory of VCFs into a single VCF.
        :summarize:
           Adds new INFO fields and FORMAT tags that combine variant data from the
           merged VCF.
        :expand:
           Explodes a VCF file into a tab-delimited file.
        
        For help on a specific subcommand:
        
        ::
        
           $ jacquard <subcommand> --help
        
        
        See `ReadTheDocs <http://jacquard.readthedocs.org/>`_ for full documentation.
        
        ====
        
        Email bfx-jacquard@umich.edu for support and questions.
        
        UM BRCF Bioinformatics Core
        
        
        
        .. _installing-jacquard:
        
        Installing Jaquard
        ==================
        Jacquard has been tested with Python 2.7 and 3.4 on Windows7, OSX, and \*nix.
        
        Prerequisites
        -------------
        .. note:: Pip installs all required libraries; see [Installing] below.
        
        
        * natsort (3.5.2)  
        * nosetests, testfixtures (3.0.2), and numpy (>=1.7.1) are required for running
          automated tests
        
        Installing
        ----------
        The easiest way to install Jacquard is through PyPI. Get pip if it's
        not available in your system:
        
        ::
        
           $ pip install jacquard
        
        
        You can install from source from github:
        
        ::
        
           $ pip install git+https://github.com/umich-brcf-bioinf/Jacquard
        
        
        If you don't have root permissions, you can install locally:
        
        ::
        
           $ pip install --user jacquard
        
        .. note:: You may need to modify your path to include the Python install dir
                 (e.g. /Users/<username>/.local/bin)
        
        
        
        Changelog
        =========
        
        0.42 (X/X/XXXX)
        ---------------
        - Added docs on readthedocs.
        - Improved workflow documentation with example data
        - *Merge* will now disambiguate tag collisions from multiple VCs
        - *Translate*/*summarize* now supports GT tags
        - Extended precision to 4 decimal places to support analysis of gene-panels.
        - Adjusted translate to handle empty high-confidence VarScan files.
        
        0.41 (5/7/2015)
        ---------------
         - Combined *filter* command with *merge* command
         - Extended *expand* to create simple metaheader glossary
         - Adjusted code to support Python >=2.7 or 3.x
         - Improved checks for consistent VCF file sets
         - Fixed bug in *merge* that caused error if any VCFs were unsorted
         - Fixed bug in *summarize* that caused error if variant was called by subset
           of callers 
        
        0.31 (3/17/2015)
        ----------------
         - Downgraded VCF format from 4.2 to 4.1
         - Fixed a bug that omitted CALLERS_REPORTED_LIST summary tag
         - Simplified summary tags; removed dependency on numpy
         - Adjusted VarScan translation to accept a file pattern to identify
           high-confidence files 
        
        
        0.3 (3/9/2015)
        --------------
         - Replaced *normalize*, *tag* commands with *translate*; relaxed constraints
           on incoming data.
         - Renamed *consensus* to *summarize*
         - More consistent behavior in *expand*
         - Significantly improved *merge* performance 
         - Added new summary tags:
           - CALLERS_REPORTED_COUNT
           - CALLERS_REPORTED_LIST
           - SAMPLES_REPORTED_COUNT
           - CALLERS_PASSED_COUNT
           - CALLERS_PASSED_LIST
           - SAMPLES_PASSED_COUNT
         - Fixed bug in how Strelka calculated AF on indels
         - Improved command validation and error handling
         - Added project/code documentation 
         - Removed dependencies on pandas
          
          
        0.21 (10/2014)
        --------------
         - Initial public release
        
        
        
        
        Jacquard is written and maintained by the University of Michigan 
        BRCF Bioinformatic Core; individual contributors include:
        
        - Jessica Bene
        - Ashwini Bhasi
        - Chris Gates
        - Divya Kriti
        - Kevin Meng
        - Peter Ulintz
Keywords: VCF bioinformatic exome-seq DNA-seq variant-call-format
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
