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

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").
.
BCCA is willing to license the Product to You only if You accept the
terms and conditions of this Agreement. By clicking on the "I ACCEPT"
button, or by copying, downloading, accessing or otherwise using the
Product, You automatically agree to be bound by the terms of this
Agreement. IF YOU DO NOT WISH TO BE BOUND BY THE TERMS OF THIS
AGREEMENT, DO NOT COPY, DOWNLOAD, ACCESS OR OTHERWISE USE THE
PRODUCT.
.
1. AUTHORITY: In the event that You are an educational institution or
organization, Your representative who is clicking the "I ACCEPT"
button, or otherwise copying, downloading, accessing or using the
Product hereby, in their personal capacity, represents and warrants
that they possess the legal authority to enter into this Agreement
on Your behalf and to bind You to the terms of this Agreement.
.
2. LICENSE TO USE: BCCA hereby grants to You a personal, non-exclusive,
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
copy of the Product installed on a single common machine or cluster of
machines may be shared for internal use by Qualified Users only. In
order to be a "Qualified User", an individual must be a student,
researcher, professor, instructor or staff member of a non-profit
educational institution or organization who uses the Product solely for
non-profit research or educational purposes.
.
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;
(b) modify, adapt, decompile, disassemble, translate into another
computer language, create derivative works of, or otherwise reverse
engineer the Product, or disclose any trade secrets relating to the
Product, except as permitted in Section 5;
(c) license, sublicense, distribute, sell, lease, transfer, assign,
trade, rent or publish the Product or any part thereof and/or copies
thereof, to any third party;
(d) use the Product to process any data other than Your own;
(e) use the Product or any part thereof for any commercial or
for-profit purpose or any other purpose other than as permitted in
Section 2; or
(f) use, without its express permission, the name of BCCA.
.
4. INTELLECTUAL PROPERTY RIGHTS: Subject to Section 5 below, all
patents, copyrights, trade secrets, service marks, trademarks and
other proprietary rights in or related to the Product and any
improvements, modifications and enhancements thereof are and will
remain the exclusive property of BCCA or its licensors. You agree
that You will not, either during or after the termination of this
Agreement, contest or challenge the title to or the intellectual
property rights of BCCA or its licensors in the Product or any
portion thereof.
.
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
and educational purposes only and You shall be the owner of those
Improvements that You directly make and of all intellectual
property rights to such Improvements, subject to the foregoing
limits on Your use and distribution of such Improvements. You
hereby grant to BCCA a perpetual, non-exclusive, worldwide,
fully-paid, irrevocable license to use such Improvements for any
purposes whatsoever, and to sublicense such Improvements including
the right for third parties to sublicense the same, in perpetuity
to the extent such rights are not limited in duration under
applicable law, without identifying or seeking Your
consent. Notwithstanding the foregoing, You acknowledge that BCCA
and its licensors will retain or own all rights in and to any
pre-existing code or other technology, content and data that may be
incorporated in the Improvements. For greater certainty, this
Section applies solely to the Source Code and shall not give You
any rights with respect to the object code or any other portion or
format of the Product which use, for greater certainty, is limited
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.
.
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
precautions necessary to safeguard the confidentiality of the
Product, and will not disclose any information about the Product to
any other person without BCCA's prior written consent. You will
not allow the removal or defacement of any confidential or
proprietary notice placed on the Product. You acknowledge that any
breach of this Section 6 will cause irreparable harm to BCCA and
its licensors.
.
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.
.
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
COMPETENT JURISDICTION REQUIRE LIABILITIES BEYOND AND DESPITE THESE
LIMITATIONS, EXCLUSIONS AND DISCLAIMERS, THESE LIMITATIONS, EXCLUSIONS
AND DISCLAIMERS SHALL APPLY WHETHER AN ACTION, CLAIM OR DEMAND ARISES
FROM A BREACH OF WARRANTY OR CONDITION, BREACH OF CONTRACT,
NEGLIGENCE, STRICT LIABILITY OR ANY OTHER KIND OF CIVIL OR STATUTORY
LIABILITY CONNECTED WITH OR ARISING FROM THIS AGREEMENT. YOU AGREE
THAT THE FOREGOING DISCLAIMER OF WARRANTIES AND LIMITATION OF
LIABILITY ARE FAIR IN LIGHT OF THE NATURE OF THE RIGHTS GRANTED HEREIN
AND THE AMOUNT OF FEES PAID BY YOU IN RESPECT OF THE PRODUCT.
.
9. INDEMNITY: You will indemnify, defend and hold harmless BCCA, its
board of directors, staff and agents from and against any and all
liability, loss, damage, action, claim or expense (including
attorney's fees and costs at trial and appellate levels) in
connection with any claim, suit, action, demand or judgement
(collectively, "Claim") arising out of, connected with, resulting
from, or sustained as a result of Your use of the Product or the
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.
.
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.
.
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.
.
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
and your staff; and (iii) developing new and enhancing existing
products. You further agree that we may provide this information to
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/* DistanceEst/* ParseAligns/*
Copyright: Copyright 2012 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: 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.

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'.