Metadata-Version: 2.4
Name: CrossMap
Version: 0.7.4
Summary: Convert genomic coordinates, annotations, and alignments between genome assemblies.
Author-email: Liguo Wang <wangliguo78@gmail.com>
License: CrossMap is a program for converting genome coordinates between different
        genome assembly versions.
        
        Copyright (C) 2014–2026 Liguo Wang
        
        This program is free software: you may redistribute it and/or modify it under
        the terms of the GNU General Public License as published by the Free Software
        Foundation, either version 3 of the License, or, at your option, any later
        version.
        
        This program is distributed in the hope that it will be useful, but WITHOUT
        ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
        FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
        
        You should have received a copy of the GNU General Public License along with
        this program. If not, see <https://www.gnu.org/licenses/>.
        
Project-URL: Homepage, https://github.com/liguowang/CrossMap
Project-URL: Documentation, https://crossmap.readthedocs.io/
Project-URL: Repository, https://github.com/liguowang/CrossMap
Project-URL: Issues, https://github.com/liguowang/CrossMap/issues
Keywords: genome,genomics,liftover,bioinformatics,assembly
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/x-rst
License-File: LICENSE.txt
Requires-Dist: pysam>=0.22
Requires-Dist: bx-python>=0.11
Requires-Dist: pyBigWig>=0.3.22
Provides-Extra: docs
Requires-Dist: sphinx>=7.2; extra == "docs"
Requires-Dist: sphinx_rtd_theme>=2.0; extra == "docs"
Dynamic: license-file

|docs| |bioconda| |galaxy|

CrossMap
=========

CrossMap is a command-line tool for converting genomic coordinates,
annotation files, and sequencing alignments between genome assemblies
using UCSC chain files.

CrossMap supports many commonly used genomics file formats, including

* BED
* GFF/GTF
* VCF
* BAM/CRAM
* BigWig
* Wiggle
* BEDGraph

Installation
============

Install the latest release from PyPI:

::

    pip install CrossMap

Or install the latest development version from GitHub:

::

    pip install git+https://github.com/liguowang/CrossMap.git

Documentation
=============

https://crossmap.readthedocs.io/

Source code
===========

https://github.com/liguowang/CrossMap

Example
=======

Convert a BED file from hg19 to hg38:

::

    CrossMap bed hg19ToHg38.over.chain.gz input.bed output.bed

License
=======

CrossMap is distributed under the GNU General Public License v3.0 or later (GPL-3.0-or-later).

.. |docs| image:: https://readthedocs.org/projects/crossmap/badge/?version=latest
   :target: https://crossmap.readthedocs.io/
   :alt: Documentation Status

.. |bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg
   :target: https://bioconda.github.io/recipes/crossmap/README.html
   :alt: Install with Bioconda

.. |galaxy| image:: https://img.shields.io/badge/Galaxy-use-blue
   :target: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/crossmap_bam/crossmap_bam/
   :alt: Available on Galaxy
