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LICENSE
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Supplementary CSIRO Open Source Software Licence v1.0
===============================================================
This document is the Supplementary Licence described in the CSIRO Open Source Software Licence, a copy of which can be found below.
The Software being licensed is 'VariantSpark'
Third Party Components
----------------------
The third party components listed below 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.
Scala
Copyright (c) 2002-2016 EPFL
Copyright (c) 2011-2016 Lightbend, Inc. (formerly Typesafe, Inc.)
Scala License (http://www.scala-lang.org/license.html)
Apache Spark (http://spark.apache.org/)
Copyright 2014 and onwards The Apache Software Foundation.
Apache License Version 2.0 (https://github.com/apache/spark/blob/master/LICENSE)
htsjdk (https://samtools.github.io/htsjdk/)
Copyright (c) 2007 and onwards by The Broad Institute, Inc
MIT, Public Domain, GNU Lesser General Public License (LGPL) Version 2.1 (https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt)
args4j (http://args4j.kohsuke.org/)
Copyright 2003-2016 Kohsuke Kawaguchi
MIT (https://opensource.org/licenses/mit-license.php)
Joda-Time (http://www.joda.org/joda-time/)
Copyright 2002-2016 Joda.org. All Rights Reserved.
Apache License Version 2.0 (https://www.joda.org/joda-time/licenses.html)
fastutil (http://fastutil.di.unimi.it/)
Copyright 2003-2016 Paolo Boldi and Sebastiano Vigna
Apache License Version 2.0 (https://github.com/vigna/fastutil/blob/master/LICENSE-2.0)
scala-csv (https://github.com/tototoshi/scala-csv)
Copyright 2013-2015 Toshiyuki Takahashi https://github.com/tototoshi/scala-csv
Apache License Version 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
CSIRO Open Source Software Licence v1.0
=======================================
(Based on MIT/BSD Open Source Licence)
IMPORTANT – PLEASE READ CAREFULLY
This document contains the terms under which CSIRO agrees to licence its Software to you. This is a template and further information relevant to the licence is set out in the Supplementary Licence specific to the Software you are licensing from CSIRO. Both documents together form this agreement.
The Software is copyright (c) Commonwealth Scientific and Industrial Research Organisation (CSIRO) ABN 41 687 119 230.
Redistribution and use of this Software in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
• Neither the name of CSIRO nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission of CSIRO.
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.
If you intend to access the Software in connection with your employment or as an agent for a principal, you should only accept this agreement if you have been authorised to do so by your employer or principal (as applicable). By accepting this agreement, you are warranting to CSIRO that you are authorised to do so on behalf of your employer or principal (as applicable).
The Software may contain third party material obtained by CSIRO under licence. Your rights to such material as part of the Software under this agreement is subject to any separate licence terms identified by CSIRO as part of the Software release - including as part of the Supplementary Licence, or as a separate file. Those third party licence terms may require you to download the relevant software from a third party site, or may mean that the third party licensor (and not CSIRO) grants you a licence directly for those components of the Software. It is your responsibility to ensure that you have the necessary rights to such third party material.