COPYRIGHT

Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: ABySS
Upstream-Contact: Shaun Jackman <sjackman@gmail.com>
Source: http://www.bcgsc.ca/platform/bioinfo/software/abyss

License: BCCA-Academic
 Debian may redistribute this software package.
 .
 BC CANCER AGENCY SOFTWARE LICENSE AGREEMENT (ACADEMIC USE)
 CAREFULLY READ THE FOLLOWING TERMS AND CONDITIONS. This License
 Agreement (the "Agreement") is a legal contract between you, your
 employer, educational institution or organization (collectively, "You")
 and the British Columbia Cancer Agency ("BCCA") with respect to the
 license of the software, including all associated documentation
 (collectively, the "Product").
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 BCCA is willing to license the Product to You only if You accept the
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 Product, You automatically agree to be bound by the terms of this
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 PRODUCT.
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 1. AUTHORITY: In the event that You are an educational institution or
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 non-transferable, limited license to use the Product solely for
 internal, non-commercial use for non-profit research or educational
 purposes only on the terms and conditions contained in this Agreement.
 The Product may be installed at a single site at Your premises only. A
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 order to be a "Qualified User", an individual must be a student,
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 3. RESTRICTIONS: You acknowledge and agree that You shall not, and
 shall not authorize any third party to:
 (a) make copies of the Product, except as provided in Section 2 and
 except for a single backup copy, and any such copy together with the
 original must be kept in Your possession or control;
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 (d) use the Product to process any data other than Your own;
 (e) use the Product or any part thereof for any commercial or
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 Section 2; or
 (f) use, without its express permission, the name of BCCA.
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 other proprietary rights in or related to the Product and any
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 5. OWNERSHIP OF IMPROVEMENTS: In the event that the Product, in the
 form provided to You, includes source code (the "Source Code"),
 You are entitled to make improvements, modifications and
 enhancements to the Source Code (collectively, "Improvements")
 which Improvements are to be used by You for non-profit research
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 Improvements that You directly make and of all intellectual
 property rights to such Improvements, subject to the foregoing
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 hereby grant to BCCA a perpetual, non-exclusive, worldwide,
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 to the extent such rights are not limited in duration under
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 incorporated in the Improvements. For greater certainty, this
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 as set forth in this Agreement including as set out in Section 3(b)
 above. You acknowledge and agree that you will provide copies of
 Improvements to BCCA in such format as reasonably requested by BCCA
 at any time upon the request of BCCA.
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 6. CONFIDENTIALITY: You acknowledge that the Product is and
 incorporates confidential and proprietary information developed,
 acquired by or licensed to BCCA. You will take all reasonable
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 Product, and will not disclose any information about the Product to
 any other person without BCCA's prior written consent. You will
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 7. NO WARRANTIES: THIS PRODUCT IS PROVIDED TO YOU BY BCCA IN ORDER TO
 ALLOW YOU TO OBTAIN ACCESS TO LEADING ACADEMIC RESEARCH. THE PRODUCT
 IS PROVIDED TO YOU ON AN "AS IS" BASIS WITHOUT WARRANTY OF ANY
 KIND. NO WARRANTY, REPRESENTATION OR CONDITION EITHER EXPRESS OR
 IMPLIED, INCLUDING WITHOUT LIMITATION, ANY IMPLIED WARRANTY OR
 CONDITION OF MERCHANTABILITY, NON-INFRINGEMENT, PERFORMANCE,
 DURABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR USE SHALL
 APPLY. BCCA DOES NOT WARRANT THAT THE PRODUCT WILL OPERATE ON A
 CONTINUOUS OR TROUBLE FREE BASIS.
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 8. LIMITATION OF LIABILITY: TO THE MAXIMUM EXTENT PERMITTED BY
 APPLICABLE LAW, IN NO EVENT SHALL THE AGGREGATE LIABILITY OF BCCA TO
 YOU EXCEED THE AMOUNT YOU HAVE PAID TO ACQUIRE THE PRODUCT ("MAXIMUM
 AMOUNT") AND WHERE YOU HAVE NOT PAID ANY AMOUNT FOR THE PRODUCT THEN
 THE MAXIMUM AMOUNT SHALL BE DEEMED TO BE CDN$100.00. IN NO EVENT SHALL
 BCCA BE LIABLE FOR ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL, OR SPECIAL
 DAMAGES, INCLUDING WITHOUT LIMITATION ANY DAMAGES FOR LOST PROFITS OR
 SAVINGS, REGARDLESS OF WHETHER THEY HAVE BEEN ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE. EXCEPT TO THE EXTENT THAT THE LAWS OF A
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 LIABILITY CONNECTED WITH OR ARISING FROM THIS AGREEMENT. YOU AGREE
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 AND THE AMOUNT OF FEES PAID BY YOU IN RESPECT OF THE PRODUCT.
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 board of directors, staff and agents from and against any and all
 liability, loss, damage, action, claim or expense (including
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 downloading of the Product, including without limitation, any Claim
 relating to infringement of BCCA's intellectual property rights or
 the intellectual property rights of any third party.
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 10. SUPPORT AND MAINTENANCE: You acknowledge and agree that, unless
 and to the extent expressly agreed by BCCA in a separate written
 document, the Product is provided to You without any support or
 maintenance from BCCA and, for greater certainty, BCCA shall have
 no obligation to issue any update or upgrade to any Product.
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 11. TERM: This Agreement is effective until terminated. You may
 terminate this Agreement at any time by ceasing use of the Product
 and destroying or deleting any copies of the Product. This
 Agreement will terminate immediately without notice from BCCA if
 You fail to comply with any provision of this Agreement. BCCA may
 terminate this Agreement at any time upon notice to you where BCCA
 determines, in its sole discretion, that any continued use of the
 Product could infringe the rights of any third parties. Upon
 termination of this Agreement, and in any event upon BCCA
 delivering You notice of termination, You shall immediately purge
 all Products from Your computer system(s), return to BCCA all
 copies of the Product that are in Your possession or control, and
 cease any further development of any Improvements. On any
 termination of this Agreement Sections 1, 4, 6, 7, 8, 9, 13 and 14
 shall survive such termination.
 .
 12. GOVERNMENT END USERS: Where any of the Product is used, duplicated
 or disclosed by or to the United States government or a government
 contractor or sub contractor, it is provided with RESTRICTED
 RIGHTS as defined in Title 48 CFR 52.227-19 and is subject to the
 following: Title 48 CFR 2.101, 52.227-19, 227.7201 through
 227.7202-4, FAR 52.227-14, and FAR 52.227-19(c)(1-2) and (6/87),
 and where applicable, the customary software license, as described
 in Title 48 CFR 227-7202 with respect to commercial software and
 commercial software documentation including DFAR 252.227-7013,
 DFAR 252,227-7014, DFAR 252.227-7015 and DFAR 252.7018, all as
 applicable.
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 13. USE OF THE DOWNLOAD SERVICE: You acknowledge and agree that you
 will be responsible for all costs, charges and taxes (where
 applicable) arising out of Your use of the Product and the
 downloading of the Product. You acknowledge that You are
 responsible for supplying any hardware or software necessary to
 use the Product pursuant to this Agreement.
 .
 14. GENERAL PROVISIONS:
 (a) This Agreement will be governed by the laws of the Province of
 British Columbia, and the laws of Canada applicable therein, excluding
 any rules of private international law that lead to the application of
 the laws of any other jurisdiction. The United Nations Convention on
 Contracts for the International Sale of Goods (1980) does not apply to
 this Agreement. The courts of the Province of British Columbia shall
 have non-exclusive jurisdiction to hear any matter arising in
 connection with this Agreement.
 (b) USE OF THE PRODUCT IS PROHIBITED IN ANY JURISDICTION WHICH DOES
 NOT GIVE EFFECT TO THE TERMS OF THIS AGREEMENT.
 (c) You agree that no joint venture, partnership, employment,
 consulting or agency relationship exists between You and BCCA as a
 result of this Agreement or Your use of the Product.
 (d) You hereby consent to Your contact information and any other
 personally identifiable information that You provide to us being
 disclosed to and maintained and used by us and our business partners
 for the purposes of (i) managing and developing our respective
 businesses and operations; (ii) marketing products and services to You
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 other persons as required to satisfy any legal requirements and to any
 person that acquires some or all of the assets of BCCA. Where any of
 the personally identifiable information that You provide to us is in
 respect of individuals other than Yourself (such as Your staff) then
 You represent and warrant to use that You have obtained all necessary
 consents and authorizations from such individuals in order to comply
 with this provision. Please see the BCCA website for further
 information regarding personally identifiable information.
 (e) This Agreement is the entire Agreement between You and BCCA
 relating to this subject matter. You will not contest the validity of
 this Agreement merely because it is in electronic form. No
 modification of this Agreement will be binding, unless in writing and
 accepted by an authorized representative of each party.
 (f) The provisions of this Agreement are severable in that if any
 provision in the Agreement is determined to be invalid or
 unenforceable under any controlling body of law, that will not affect
 the validity or enforceability of the remaining provisions of the
 Agreement.
 (g) You agree to print out or download a copy of this Agreement and
 retain it for Your records.
 (h) You consent to the use of the English language in this Agreement.
 (i) You may not assign this Agreement or any of Your rights or
 obligations hereunder without BCCA's prior written consent. BCCA, at
 its sole discretion may assign this Agreement without notice to You.

Files: *
Copyright: Copyright 2013 Genome Sciences Centre
License: BCCA-Academic

Files: Common/* DataLayer/* DistanceEst/* FMIndex/* Map/* ParseAligns/*
Copyright: Copyright 2013 Genome Sciences Centre
License: BCCA-Academic or GPL-3+

Files: Common/cholesky.hpp
Copyright: Copyright 2005 Gunter Winkler, Konstantin Kutzkow
License: LGPL-2.1+

Files: Common/city.cc Common/city.h
Copyright: Copyright 2011 Google, Inc.
License: Expat

Files: Layout/*
Copyright: Copyright 2012 Shaun Jackman
License: BCCA-Academic or GPL-3+

Files: dialign/*
Copyright: Copyright 2008 Amarendran R. Subramanian
License: LGPL-2.1+

License: LGPL-2.1+
 On Debian systems, see `/usr/share/common-licenses/LGPL-2.1'.
 .
 This library is free software; you can redistribute it and/or
 modify it under the terms of the GNU Lesser General Public
 License as published by the Free Software Foundation; either
 version 2.1 of the License, or (at your option) any later version.
 .
 This library 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
 Lesser General Public License for more details.
 .
 You should have received a copy of the GNU Lesser General Public
 License along with this library; if not, write to the Free Software
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 .
 Amarendran R. Subramanian, hereby disclaims all copyright interest in the
 DIALIGN-TX (a multiple sequence alignment algorithm) written by Amarendran R. Subramanian.
 .
 Amarendran R. Subramanian, 2004-2008
 .
 DIALIGN-TX has been co-authored by Volker Menrad and Dorothea Emig.
 .
 Research work using DIALIGN-TX should cite:
 .
 DIALIGN-TX: improvement of the segment-based approach for multiple
 sequence alignment by combining greedy and progressive alignment
 strategies
 Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern,
 Algorithms for Molecular Biology 3:6, 2008
 .
 DIALIGN-T: An improved algorithm for segment-based multiple
 sequence alignment
 Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann,
 Burkhard Morgenstern, BMC Bioinformatics 6:66, 2005

Files: FMIndex/bit_array.h
Copyright: Copyright 2010 Daisuke Okanohara
License: BSD-3-clause
 Redistribution and use 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 the authors nor the names of its contributors
 may be used to endorse or promote products derived from this
 software without specific prior written permission.

Files: FMIndex/sais.hxx
Copyright: Copyright 2010 Yuta Mori
License: Expat

License: Expat
 Permission is hereby granted, free of charge, to any person
 obtaining a copy of this software and associated documentation
 files (the "Software"), to deal in the Software without
 restriction, including without limitation the rights to use,
 copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the
 Software is furnished to do so, subject to the following
 conditions:
 .
 The above copyright notice and this permission notice shall be
 included in all copies or substantial portions of the Software.
 .
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 OTHER DEALINGS IN THE SOFTWARE.

License: GPL-3+
 This program is free software; you can 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 package; if not, write to the Free
 Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 Boston, MA 02110-1301 USA
 .
 On Debian systems, the full text of the GNU General Public
 License version 3 can be found in the file
 `/usr/share/common-licenses/GPL-3'.