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CSIRO Open Source Software License Agreement (GPLv3)
Copyright (c) 2019-20, Commonwealth Scientific and Industrial Research Organisation (CSIRO) ABN 41 687 119 230.
All rights reserved. CSIRO is willing to grant you a license to Software on the terms of the GNU General Public License version 3 as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.html), except where otherwise indicated for third party material.
The following additional terms apply under clause 7 of that license:
EXCEPT AS EXPRESSLY STATED IN THIS AGREEMENT AND TO THE FULL EXTENT PERMITTED BY APPLICABLE LAW, THE SOFTWARE IS PROVIDED "AS-IS". CSIRO MAKES NO REPRESENTATIONS, WARRANTIES OR CONDITIONS OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY REPRESENTATIONS, WARRANTIES OR CONDITIONS REGARDING THE CONTENTS OR ACCURACY OF THE SOFTWARE, OR OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT, THE ABSENCE OF LATENT OR OTHER DEFECTS, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT DISCOVERABLE.
TO THE FULL EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL CSIRO BE LIABLE ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION, IN AN ACTION FOR BREACH OF CONTRACT, NEGLIGENCE OR OTHERWISE) FOR ANY CLAIM, LOSS, DAMAGES OR OTHER LIABILITY HOWSOEVER INCURRED. WITHOUT LIMITING THE SCOPE OF THE PREVIOUS SENTENCE THE EXCLUSION OF LIABILITY SHALL INCLUDE: LOSS OF PRODUCTION OR OPERATION TIME, LOSS, DAMAGE OR CORRUPTION OF DATA OR RECORDS; OR LOSS OF ANTICIPATED SAVINGS, OPPORTUNITY, REVENUE, PROFIT OR GOODWILL, OR OTHER ECONOMIC LOSS; OR ANY SPECIAL, INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES, ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT, ACCESS OF THE SOFTWARE OR ANY OTHER DEALINGS WITH THE SOFTWARE, EVEN IF CSIRO HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH CLAIM, LOSS, DAMAGES OR OTHER LIABILITY.
APPLICABLE LEGISLATION SUCH AS THE AUSTRALIAN CONSUMER LAW MAY APPLY REPRESENTATIONS, WARRANTIES, OR CONDITIONS, OR IMPOSES OBLIGATIONS OR LIABILITY ON CSIRO THAT CANNOT BE EXCLUDED, RESTRICTED OR MODIFIED TO THE FULL EXTENT SET OUT IN THE EXPRESS TERMS OF THIS CLAUSE ABOVE "CONSUMER GUARANTEES". TO THE EXTENT THAT SUCH CONSUMER GUARANTEES CONTINUE TO APPLY, THEN TO THE FULL EXTENT PERMITTED BY THE APPLICABLE LEGISLATION, THE LIABILITY OF CSIRO UNDER THE RELEVANT CONSUMER GUARANTEE IS LIMITED (WHERE PERMITTED AT CSIRO’S OPTION) TO ONE OF FOLLOWING REMEDIES OR SUBSTANTIALLY EQUIVALENT REMEDIES:
(a) THE REPLACEMENT OF THE SOFTWARE, THE SUPPLY OF EQUIVALENT SOFTWARE, OR SUPPLYING RELEVANT SERVICES AGAIN;
(b) THE REPAIR OF THE SOFTWARE;
(c) THE PAYMENT OF THE COST OF REPLACING THE SOFTWARE, OF ACQUIRING EQUIVALENT SOFTWARE, HAVING THE RELEVANT SERVICES SUPPLIED AGAIN, OR HAVING THE SOFTWARE REPAIRED.
IN THIS CLAUSE, CSIRO INCLUDES ANY THIRD PARTY AUTHOR OR OWNER OF ANY PART OF THE SOFTWARE OR MATERIAL DISTRIBUTED WITH IT. CSIRO MAY ENFORCE ANY RIGHTS ON BEHALF OF THE RELEVANT THIRD PARTY.
Third Party Components
The following third party components are distributed with the Software. You agree to comply with the license terms for these components as part of accessing the Software. Other third party software may also be identified in separate files distributed with the Software.
bcftools (v1.9)
Copyright (C) 2012-2014 Genome Research Ltd.
MIT/Expat (https://github.com/samtools/bcftools/blob/develop/LICENSE)
BEAGLE (v5.1)
Copyright: 2013-2019 Brian L. Browning
GNU General Public License v3 (https://faculty.washington.edu/browning/beagle/gpl_license)
GERMLINE (v 1.5.3)
Gusev et al. 2008 Genome Res doi: 10.1101/gr.081398.108
Apache 2.0 (https://github.com/gusevlab/germline/blob/master/LICENSE)
vcftools (v.0.1.16)
The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011
GNU Lesser General Public License v3 (https://github.com/vcftools/vcftools/blob/master/LICENSE)
python
PSF LICENSE (GPL compatible) (https://docs.python.org/3/license.html)
numpy
Copyright © 2005-2020, NumPy Developers. All rights reserved.
BSD (https://numpy.org/license.html)
https://www.scipy.org/scipylib/license.html
scipy
BSD (https://www.scipy.org/scipylib/license.html)
pandas
Copyright (c) 2008-2012, AQR Capital Management, LLC, Lambda Foundry, Inc. and PyData Development Team
BSD 3-Clause License (https://github.com/pandas-dev/pandas/blob/master/LICENSE)
pip
Copyright (c) 2008-2019 The pip developers
MIT (https://github.com/pypa/pip/blob/master/LICENSE.txt)
conda
(c) 2017 Continuum Analytics, Inc. (dba Anaconda, Inc.). https://www.anaconda.com. All Rights Reserved
BSD (https://docs.conda.io/en/latest/license.html)
snakemake
© Copyright 2014-2016, Johannes Koester
MIT (https://snakemake.readthedocs.io/en/stable/project_info/license.html)
R
GNU General Public License v3 (https://www.r-project.org/Licenses/GPL-3)
dplyr
Maintainer: Hadley Wickham <hadley at rstudio.com>
MIT (https://cran.r-project.org/web/licenses/MIT)
optparse
Maintainer: Trevor L Davis <trevor.l.davis at gmail.com>
GNU General Public License v3 (https://cran.r-project.org/web/licenses/GPL-3)
rmarkdown
Maintainer: Yihui Xie <xie at yihui.name>
GNU General Public License v3 (https://cran.r-project.org/web/licenses/GPL-3)
pandoc
Copyright (C) 2006-2019 John MacFarlane <jgm at berkeley dot edu>
GNU General Public License v2+ (https://github.com/jgm/pandoc/blob/master/COPYRIGHT)