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The source code of BISCUIT includes a number of different licenses, including
the MIT License, a Modified 3-Clause BSD License, the Apache License, and the
GNU General Public License. The specific source files and their corresponding
licenses and copyright holder(s) are listed below.
-------------------------------- src/ directory --------------------------------
[ Files in the src/ directory are distributed according to the terms of the
following MIT License. ]
The MIT License (MIT)
Copyright (c) 2016-2020 [email protected]
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.
------------------------------ lib/aln/ directory ------------------------------
[ Files in the lib/aln/ directory fall under an assortment of copyrights and
licenses, including the GNU General Public License. ]
[ Files distributed in the lib/aln/ directory that fall under the MIT License
can be found in following, as well as the copyright holders. The MIT License
text can be found above. ]
* lib/aln/kstring.h
Copyright (c) by Attractive Chaos <[email protected]>
* lib/aln/bwt.c
Copyright (c) 2008 Genome Research Ltd (GRL).
* lib/aln/mem_alnreg_format.c
Copyright (c) 2016-2020 [email protected]
* lib/aln/bwtindex.c
Copyright (c) 2008 Genome Research Ltd (GRL).
* lib/aln/utils.c
Copyright (c) 2008 Genome Research Ltd (GRL).
* lib/aln/mem_pair.c
Copyright (c) 2016-2020 [email protected]
* lib/aln/khash.h
Copyright (c) 2008, 2009, 2011 by Attractive Chaos <[email protected]>
* lib/aln/bntseq.h
Copyright (c) 2008 Genome Research Ltd (GRL).
* lib/aln/ksw.c
Copyright (c) 2011 by Attractive Chaos <[email protected]>
* lib/aln/memchain.c
Copyright (c) 2016-2020 [email protected]
Copyright (c) 2007-2014 Attractive Chaos <[email protected]>
* lib/aln/mem_alnreg.c
Copyright (c) 2016-2020 [email protected]
Copyright (c) 2007-2014 Attractive Chaos <[email protected]>
* lib/aln/ksort.h
Copyright (c) 2008, by Attractive Chaos <[email protected]>
* lib/aln/bntseq.c
Copyright (c) 2016-2020 [email protected]
Copyright (c) 2008 Genome Research Ltd (GRL).
* lib/aln/bwt.h
Copyright (c) 2008 Genome Research Ltd (GRL).
* lib/aln/kseq.h
Copyright (c) 2008, 2009, 2011 Attractive Chaos <[email protected]>
* lib/aln/kvec.h
Copyright (c) 2008, by Attractive Chaos <[email protected]>
* lib/aln/utils.h
Copyright (c) 2008 Genome Research Ltd (GRL).
* lib/aln/is.c
Copyright (c) 2008 Yuta Mori All Rights Reserved.
[ Files distributed in the lib/aln/ directory that fall under the GNU General
Public License can be found in following, as well as the copyright holders.
The GNU Genral Public License included with the code can be found below. The
full text can be found at https://opensource.org/licenses/GPL-2.0. ]
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 2
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, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
* lib/aln/bwt_gen.c
Copyright (C) 2004, Wong Chi Kwong.
[ Files distributed in the lib/aln/ directory that are believed to fall under
the GNU General Public License, but which is not explicitly referenced, can be
found in following, as well as the copyright holders. The license message has
been copied below for reference. ]
* QSufSort.c
Original source from qsufsort.c
Copyright 1999, N. Jesper Larsson, all rights reserved.
This file contains an implementation of the algorithm presented in "Faster
Suffix Sorting" by N. Jesper Larsson ([email protected]) and Kunihiko
Sadakane ([email protected]).
This software may be used freely for any purpose. However, when distributed,
the original source must be clearly stated, and, when the source code is
distributed, the copyright notice must be retained and any alterations in
the code must be clearly marked. No warranty is given regarding the quality
of this software.
Modified by Wong Chi-Kwong, 2004
Changes summary: - Used long variable and function names
- Removed global variables
- Replace pointer references with array references
- Used insertion sort in place of selection sort and increased insertion sort threshold
- Reconstructing suffix array from inverse becomes an option
- Add handling where end-of-text symbol is not necessary < all characters
- Removed codes for supporting alphabet size > number of characters
No warrenty is given regarding the quality of the modifications.
[ Files distributed in the lib/aln/ directory that fall under the 2-Clause BSD
License can be found in following, as well as the copyright holders. The
2-Clause BSD License text can be found below for reference. ]
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. 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.
THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
* lib/aln/kbtree.h
Copyright 1997-1999, 2001, John-Mark Gurney.
2008-2009, Attractive Chaos <[email protected]>
----------------------------- lib/htslib/ directory ----------------------------
[ Files in the lib/htslib/ directory fall under the MIT/Expat or the Modified
3-Clause BSD License as described in the lib/htslib/LICENSE file. A copy of
the text has been included below for reference. ]
[Files in this distribution outwith the cram/ subdirectory are distributed
according to the terms of the following MIT/Expat license.]
The MIT/Expat License
Copyright (C) 2012-2014 Genome Research Ltd.
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.
[Files within the cram/ subdirectory in this distribution are distributed
according to the terms of the following Modified 3-Clause BSD license.]
The Modified-BSD License
Copyright (C) 2012-2014 Genome Research Ltd.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. 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.
3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute
nor the names of its contributors may be used to endorse or promote products
derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR ITS CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
[The use of a range of years within a copyright notice in this distribution
should be interpreted as being equivalent to a list of years including the
first and last year specified and all consecutive years between them.
For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
2011-2012" should be interpreted as being identical to a notice that reads
"Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
that reads "Copyright (C) 2005-2012" should be interpreted as being identical
to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
2011, 2012".]
------------------------------ lib/klib/ directory -----------------------------
[ Files in the lib/klib/ directory are distributed according to the terms of the
MIT License. ]
[ Files distributed in the lib/klib/ directory that fall under the MIT License
can be found in following, as well as the copyright holders. The MIT License
text can be found above. ]
* lib/klib/kstring.h
Copyright (c) by Attractive Chaos <[email protected]>
* lib/klib/lua/klib.lua
Copyright (c) 2011, Attractive Chaos <[email protected]>
* lib/klib/knetfile.c
Copyright (c) 2008 by Genome Research Ltd (GRL).
2010 by Attractive Chaos <[email protected]>
* lib/klib/khash.h
Copyright (c) 2008, 2009, 2011 by Attractive Chaos <[email protected]>
* lib/klib/ksw.c
Copyright (c) 2011 by Attractive Chaos <[email protected]>
* lib/klib/bgzf.h
Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
2011 Attractive Chaos <[email protected]>
* lib/klib/klist.h
Copyright (c) 2008-2009, by Attractive Chaos <[email protected]>
* lib/klib/bgzf.c
Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
2011 Attractive Chaos <[email protected]>
* lib/klib/ksort.h
Copyright (c) 2008, 2011 Attractive Chaos <[email protected]>
* lib/klib/kseq.h
Copyright (c) 2008, 2009, 2011 Attractive Chaos <[email protected]>
* lib/klib/kvec.h
Copyright (c) 2008, by Attractive Chaos <[email protected]>
------------------------------ lib/sgsl/ directory -----------------------------
[ Files in the lib/sgsl/ directory are distributed according to the terms of the
GNU General Public License version 3. The text for the GNU General Public
License version 3 has been copied below for reference. ]
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
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To protect your rights, we need to prevent others from denying you
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For example, if you distribute copies of such a program, whether
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Developers that use the GNU GPL protect your rights with two steps:
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For the developers' and authors' protection, the GPL clearly explains
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Some devices are designed to deny users access to install or run
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The precise terms and conditions for copying, distribution and
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END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
{one line to give the program's name and a brief idea of what it does.}
Copyright (C) {year} {name of author}
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 program. If not, see <http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
{project} Copyright (C) {year} {fullname}
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.
----------------------------- lib/utils/ directory -----------------------------
[ Files in the lib/utils/ directory are distributed according to the terms of
the Apache License version 2.0. The text for the Apache License has been
copied below for reference. ]
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
1. Definitions.
"License" shall mean the terms and conditions for use, reproduction,
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