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. ]

[ Files have a variety of copyright holders as given below. ]

  |- src/bc.c
  |- src/bc.h
  |- src/bisc_utils.c
  |- src/bisc_utils.h
  |- src/biscuit.h
  |---- Copyright (c) 2023-2026 Jacob.Morrison@vai.org

  |- src/khashl.h
  |---- Copyright (c) 2019-2024 by Attractive Chaos <attractor@live.co.uk>

  |- src/qc.c
  |- src/qc.h
  |---- Copyright (c) 2021-2026 Jacob.Morrison@vai.org

  |- src/qc_coverage.c
  |- src/qc_coverage.h
  |---- Copyright (c) 2024-2026 Jacob.Morrison@vai.org

  |- src/asm_pairwise.c
  |- src/bamfilter.c
  |- src/bamfilter.h
  |- src/bsconv.c
  |- src/bsconv.h
  |- src/bsstrand.c
  |- src/bsstrand.h
  |- src/cinread.c
  |- src/cinread.h
  |- src/epiread.c
  |- src/epiread.h
  |- src/epiread_rectangle.c
  |- src/main.c
  |- src/mergecg.c
  |- src/pileup.c
  |- src/pileup.h
  |- src/refcache.h
  |- src/tview.c
  |- src/vcf2bed.c
  |---- Copyright (c) 2016-2020 Wanding.Zhou@vai.org
                      2021-2026 Jacob.Morrison@vai.org

The MIT License (MIT)

Copyright (c) (AS GIVEN ABOVE)

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/align.c
        Copyright (c) 2022-2026 Jacob.Morrison@vai.org
  * lib/aln/bntseq.c
        Copyright (c) 2008 Genome Research Ltd (GRL).
                      2016-2020 Wanding.Zhou@vai.org
                      2021-2026 Jacob.Morrison@vai.org
  * lib/aln/bntseq.h
        Copyright (c) 2008 Genome Research Ltd (GRL).
                      2022-2026 Jacob.Morrison@vai.org
  * lib/aln/bwa.c
        Copyright (c) 2022-2026 Jacob.Morrison@vai.org
  * lib/aln/bwa.h
        Copyright (c) 2022-2026 Jacob.Morrison@vai.org
  * lib/aln/bwamem.c
        Copyright (c) 2022-2026 Jacob.Morrison@vai.org
  * lib/aln/bwamem.h
        Copyright (c) 2022-2026 Jacob.Morrison@vai.org
  * lib/aln/bwt.c
        Copyright (c) 2008 Genome Research Ltd (GRL).
                      2022-2026 Jacob.Morrison@vai.org
  * lib/aln/bwt.h
        Copyright (c) 2008 Genome Research Ltd (GRL).
                      2022-2026 Jacob.Morrison@vai.org
  * lib/aln/bwtindex.c
        Copyright (c) 2008 Genome Research Ltd (GRL).
                      2022-2026 Jacob.Morrison@vai.org
  * lib/aln/is.c
        Copyright (c) 2008 Yuta Mori All Rights Reserved.
  * lib/aln/khash.h
        Copyright (c) 2008, 2009, 2011 by Attractive Chaos <attractor@live.co.uk>
  * lib/aln/kseq.h
        Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor@live.co.uk>
  * lib/aln/ksort.h
        Copyright (c) 2008, by Attractive Chaos <attractivechaos@aol.co.uk>
  * lib/aln/kstring.h
        Copyright (c) by Attractive Chaos <attractor@live.co.uk> 
  * lib/aln/ksw.c
        Copyright (c) 2011 by Attractive Chaos <attractor@live.co.uk>
  * lib/aln/kvec.h
        Copyright (c) 2008, by Attractive Chaos <attractor@live.co.uk>
  * lib/aln/mem_alnreg.c
        Copyright (c) 2007-2014 Attractive Chaos <attractor@live.co.uk>
                      2016-2020 Wanding.Zhou@vai.org
                      2021-2026 Jacob.Morrison@vai.org
  * lib/aln/mem_alnreg_format.c
        Copyright (c) 2016-2020 Wanding.Zhou@vai.org
                      2021-2026 Jacob.Morrison@vai.org
  * lib/aln/mem_pair.c
        Copyright (c) 2016-2020 Wanding.Zhou@vai.org
                      2021-2026 Jacob.Morrison@vai.org
  * lib/aln/memchain.c
        Copyright (c) 2007-2014 Attractive Chaos <attractor@live.co.uk>
                      2016-2020 Wanding.Zhou@vai.org
                      2021-2026 Jacob.Morrison@vai.org
  * lib/aln/utils.c
        Copyright (c) 2008 Genome Research Ltd (GRL).
                      2022-2026 Jacob.Morrison@vai.org
  * lib/aln/utils.h
        Copyright (c) 2008 Genome Research Ltd (GRL).
                      2022-2026 Jacob.Morrison@vai.org

[ 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 (jesper@cs.lth.se) and Kunihiko
        Sadakane (sada@is.s.u-tokyo.ac.jp).
        
        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 <attractor@live.co.uk>


