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debian/changelog
View file @ de5a3207
libmaus2 (2.0.611-1) UNRELEASED; urgency=medium
* Initial release (Closes: #<bug>)
* Initial release (Closes: #926964)
-- Andreas Tille <tille@debian.org> Fri, 12 Apr 2019 10:26:19 +0200
-- Andreas Tille <tille@debian.org> Fri, 12 Apr 2019 22:45:58 +0200
debian/control
View file @ de5a3207
......@@ -34,7 +34,7 @@ Depends: libmaus2-2 (= ${binary:Version}),
zlib1g-dev,
${shlibs:Depends},
${misc:Depends}
Description: collection of data structures and algorithms for biobambam
Description: collection of data structures and algorithms for biobambam (devel)
Libmaus2 is a collection of data structures and algorithms. It contains
.
* I/O classes (single byte and UTF-8)
......@@ -43,3 +43,5 @@ Description: collection of data structures and algorithms for biobambam
* BAM sequence alignment files input/output (simple and collating)
.
and many lower level support classes.
.
This package contains header files and static libraries.
debian/copyright
View file @ de5a3207
......@@ -31,21 +31,188 @@ Copyright: 2007-2012 Simon Gog (SDSL library)
2011-2013 Genome Research Limited
License: GPL-3
radixsort code in src/libmaus2/sorting/SerialRadixSort64.hpp adapted from code by Andrew I. Schein (see file for license)
divsufsort code in src/libmaus2/suffixsort/divsufsort* by Yuta Mori (see file for license)
SAIS code in src/libmaus2/suffixsort/SAIS_Mori.hpp by Yuta Mori (see file for license)
md5 code in src/libmaus2/digest/md5.[ch] by L. Peter Deutsch (Aladdin Enterprises) (see file for license)
some code in src/libmaus2/bambam/DuplicationMetrics.hpp is imported from the Picard project (MIT license, see file for copyright)
LZ4 code in src/libmaus2/lz/lz4.[ch] by Yann Collect (BSD 2-Clause licence, see files)
CRC32 code in src/libmaus2/hashing/Crc3.{cpp/hpp} by Stephan Brumme (ZLib type license, see files)
libmaus2/digest/sha(256|512)_*.asm (Intel license, see files)
Part of CRC32{|C} code in src/libmaus2/digest/CRC32{|C}_Core.cpp by Mark Adler (see file for license)
Part of CRC32{|C} code in src/libmaus2/digest/CRC32{|C}_Core.cpp by Cisco Systems, Inc. and Herbert Xu (GPLv2)
Hash code in src/libmaus2/hashing/MurmurHash3.{cpp|h} and libmaus2/digest/MurmurHash3_x64_128.hpp by Austin Appleby (public domain)
Rest by German Tischler published under GPLv2/GPLv3 (some of it written while at Genome Research Limited/WTSI)
Files: src/libmaus2/sorting/SerialRadixSort64.hpp
Copyright: 2008, 2009 Andrew I. Schein
2010, German Tischler, Solon Pissis
2010-2013 German Tischler
2011-2013 Genome Research Limited
License: MIT
Files: src/libmaus2/suffixsort/divsufsort*
Copyright: 2003-2008 Yuta Mori
2011-2013 German Tischler
2011-2013 Genome Research Limited
License: MIT
Files: src/libmaus2/suffixsort/SAIS_Mori.hpp
Copyright: 2008-2010 Yuta Mori
2011-2013 German Tischler
2011-2013 Genome Research Limited
License: MIT
Files: src/libmaus2/digest/md5*
Copyright: 1999, 2000, 2002 L. Peter Deutsch <ghost@aladdin.com> (Aladdin Enterprises)
License: as-is
This software is provided 'as-is', without any express or implied
warranty. In no event will the authors be held liable for any damages
arising from the use of this software.
.
Permission is granted to anyone to use this software for any purpose,
including commercial applications, and to alter it and redistribute it
freely, subject to the following restrictions:
.
1. The origin of this software must not be misrepresented; you must not
claim that you wrote the original software. If you use this software
in a product, an acknowledgment in the product documentation would be
appreciated but is not required.
2. Altered source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
3. This notice may not be removed or altered from any source distribution.
Files: src/libmaus2/bambam/DuplicationMetrics*
Copyright: 2009 The Broad Institute
2013 German Tischler
2013 Genome Research Limited
License: MIT
Files: src/libmaus2/lz/lz4*
Copyright: 2011-2013 Yann Collet
License: BSD-2-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.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 COPYRIGHT
OWNER 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.
Files: src/libmaus2/hashing/Crc3*
Copyright: 2011-2013 Stephan Brumme
License: zlib
* This software is provided 'as-is', without any express or implied warranty.
In no event will the author be held liable for any damages arising from the
use of this software.
* Permission is granted to anyone to use this software for any purpose,
including commercial applications, and to alter it and redistribute it
freely, subject to the following restrictions:
* The origin of this software must not be misrepresented; you must not claim
that you wrote the original software.
* If you use this software in a product, an acknowledgment in the product
documentation would be appreciated but is not required.
* Altered source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
Files: src/libmaus2/digest/*.asm
Copyright: 2012, Intel Corporation
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 Intel Corporation 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 INTEL CORPORATION "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 INTEL CORPORATION 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.
Files: src/libmaus2/digest/CRC32*_Core.*
Copyright: 2013 Mark Adler <madler@alumni.caltech.edu>
2004 Cisco Systems, Inc.
2008 Herbert Xu <herbert@gondor.apana.org.au>
2014 German Tischler
License: as-is+gpl-2+
The copyright by Mark Adler is licensed "as-is":
.
This software is provided 'as-is', without any express or implied
warranty. In no event will the author be held liable for any damages
arising from the use of this software.
.
Permission is granted to anyone to use this software for any purpose,
including commercial applications, and to alter it and redistribute it
freely, subject to the following restrictions:
.
1. The origin of this software must not be misrepresented; you must not
claim that you wrote the original software. If you use this software
in a product, an acknowledgment in the product documentation would be
appreciated but is not required.
2. Altered source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
3. This notice may not be removed or altered from any source distribution.
.
.
The part copyright by Cisco Systems, Inc. / Herbert Xu is GPL-2+
Files: src/libmaus2/hashing/MurmurHash3*
src/libmaus2/digest/MurmurHash3*
Copyright: Austin Appleby (public domain)
License: public-domain2
MurmurHash3 was written by Austin Appleby, and is placed in the public
domain. The author hereby disclaims copyright to this source code.
Files: debian/*
Copyright: 2019 Andreas Tille <tille@debian.org>
License: GPL-3+
License: MIT
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.
.
On Debian systems you can find the full text of the GNU General Public
License version 3 at /usr/share/common-licenses/GPL-3.