Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: SPAdes Upstream-Contact: spades.support@bioinf.spbau.ru Source: https://github.com/ablab/spades Files-Excluded: **/bamtools **/nlopt **/ssw ext/include/boost ext/include/cuckoo ext/include/llvm/Support/ConvertUTF.h ext/include/parallel_hashmap ext/include/samtools/misc/ace2sam ext/include/samtools/misc/maq2sam-long ext/include/samtools/misc/maq2sam-short ext/include/samtools/misc/md5fa ext/include/samtools/misc/md5sum-lite ext/include/samtools/misc/wgsim ext/src/samtools/misc/ace2sam ext/src/samtools/misc/maq2sam-long ext/src/samtools/misc/maq2sam-short ext/src/samtools/misc/md5fa ext/src/samtools/misc/md5sum-lite ext/src/samtools/misc/wgsim ext/include/xxh ext/src/googletest ext/src/llvm/ConvertUTF.cpp ext/src/ncbi ext/src/python_libs ext/src/spoa src/tools/webvis .gitignore Files: * Copyright: 2023-2024, SPAdes team 2015-2022 Saint Petersburg State University 2011-2014 Saint Petersburg Academic University License: GPL-2 Files: ext/include/blaze/* Copyright: 2012-2020 Klaus Iglberger License: BSD-3-clause Files: ext/include/boomphf/BooPHF.h Copyright: 2015 Guillaume Rizk License: Expat Comment: MIT licensed as part of BBHash (https://github.com/rizkg/BBHash) Files: ext/include/bwa/bntseq.h ext/include/bwa/bwt.h ext/include/bwa/utils.h Copyright: 2008-2010 Genome Research Ltd (GRL). 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License: Expat Files: ext/include/samtools/misc/md5.c Copyright: 1995 Colin Plumb License: public-domain Files: ext/include/samtools/misc/wgsim.c Copyright: 2008-2010 Genome Research Ltd (GRL). License: Expat Files: ext/include/samtools/razf.h Copyright: 2008 ruanjue@gmail.com>, Heng Li License: BSD-2-clause Files: ext/include/samtools/win32/zconf.h Copyright: 1995-2005 Jean-loup Gailly. License: Zlib Files: ext/include/samtools/win32/zlib.h Copyright: 1995-2022 Jean-loup Gailly and Mark Adler License: Zlib Files: ext/include/sse2neon/* Copyright: John W. Ratcliff , Brandon Rowlett , Ken Fast , Eric van Beurden , Alexander Potylitsin , Hasindu Gamaarachchi , Jim Huang , Mark Cheng , Malcolm James MacLeod , Devin Hussey (easyaspi314) , Sebastian Pop , Developer Ecosystem Engineering , Danila Kutenin , François Turban (JishinMaster) , Pei-Hsuan Hung , Yang-Hao Yuan , Syoyo Fujita , Brecht Van Lommel License: Expat Files: ext/include/teamcity_gtest/* Copyright: 2015 Paul Shmakov License: Apache-2.0 Files: ext/include/teamcity_gtest/teamcity_messages.h Copyright: 2011 JetBrains s.r.o. License: Apache-2.0 Files: ext/include/threadpool/* Copyright: 2018 Loic Reyreaud License: Expat Files: ext/include/tsl/* Copyright: 2017 Thibaut Goetghebuer-Planchon License: Expat Files: ext/src/bwa/CMakeLists.txt Copyright: 2016, 2017, 2019, Saint Petersburg State University License: Apache-2.0 Files: ext/src/bwa/bntseq.c ext/src/bwa/bwt.c ext/src/bwa/bwtindex.c ext/src/bwa/utils.c Copyright: 2008-2010 Genome Research Ltd (GRL). 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Eddy 1992-2004 Washington University School of Medicine 1992-1994 MRC Laboratory of Molecular Biology License: BSD-3-clause Files: ext/src/hmmer/libdivsufsort/* Copyright: 2003-2008 Yuta Mori License: Expat or X11 Files: ext/src/hmmer/libdivsufsort/COPYING ext/src/hmmer/libdivsufsort/divsufsort.c ext/src/hmmer/libdivsufsort/divsufsort.h.in Copyright: 2003-2008 Yuta Mori License: Expat Files: ext/src/lexy/* Copyright: 2020-2024, Jonathan Müller and lexy contributors License: BSL-1.0 Files: ext/src/llvm/MD5.cpp Copyright: 2001 Alexander Peslyak License: public-domain Files: ext/src/llvm/regcomp.c ext/src/llvm/regengine.inc ext/src/llvm/regerror.c ext/src/llvm/regex2.h ext/src/llvm/regex_impl.h ext/src/llvm/regexec.c ext/src/llvm/regfree.c ext/src/llvm/regutils.h Copyright: 1992-1994 The Regents of the University of California. 1992-1994 Henry Spencer. License: BSD-3-clause Files: ext/src/llvm/regstrlcpy.c Copyright: 1998 Todd C. 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License: Expat Files: ext/src/samtools/bcftools/bcf.h Copyright: 2010 Broad Institute License: Expat Files: ext/src/samtools/bcftools/kmin.c ext/src/samtools/bcftools/kmin.h Copyright: 2008-2011 Attractive Chaos License: Expat Files: ext/src/samtools/bgzf.c ext/src/samtools/bgzf.h ext/src/samtools/bgzip.c Copyright: Massachusetts Institute of Technology 2008, Broad Institute License: Expat Files: ext/src/samtools/kaln.c ext/src/samtools/kaln.h ext/src/samtools/kprobaln.c ext/src/samtools/kprobaln.h Copyright: 2003-2011 Heng Li License: Expat Files: ext/src/samtools/khash.h ext/src/samtools/kseq.h ext/src/samtools/kstring.h Copyright: 2008-2011 Attractive Chaos License: Expat Files: ext/src/samtools/misc/CMakeLists.txt Copyright: 2010 Derek Barnett License: Expat Files: ext/src/samtools/misc/ace2sam.c Copyright: 2003-2011 Heng Li License: Expat Files: ext/src/samtools/misc/export2sam.pl Copyright: 2010 Illumina, Inc. 2008-2009 Genome Research Ltd. License: Expat Files: ext/src/samtools/misc/md5.c Copyright: 1993 Colin Plumb License: public-domain Files: ext/src/samtools/misc/wgsim.c Copyright: 2008-2010 Genome Research Ltd (GRL). License: Expat Files: ext/src/samtools/razf.c ext/src/samtools/razf.h Copyright: 2008 ruanjue@gmail.com>, Heng Li License: BSD-2-clause Files: ext/src/samtools/win32/zconf.h Copyright: 1995-2005 Jean-loup Gailly. License: Zlib Files: ext/src/samtools/win32/zlib.h Copyright: 1995-2022 Jean-loup Gailly and Mark Adler License: Zlib Files: ext/src/teamcity_gtest/CMakeLists.txt Copyright: 2016-2019 Saint Petersburg State University License: Apache-2.0 Files: ext/src/teamcity_gtest/teamcity_gtest.cpp Copyright: 2015, Paul Shmakov License: Apache-2.0 Files: ext/src/teamcity_gtest/teamcity_messages.cpp Copyright: 2011 JetBrains s.r.o. License: Apache-2.0 Files: ext/src/zlib-ng/* Copyright: 1995-2022 Jean-loup Gailly and Mark Adler License: Zlib Files: ext/src/zlib-ng/adler32.c ext/src/zlib-ng/adler32_p.h ext/src/zlib-ng/crc32_braid.c ext/src/zlib-ng/crc32_braid_comb.c ext/src/zlib-ng/gzguts.h ext/src/zlib-ng/gzlib.c ext/src/zlib-ng/gzread.c.in ext/src/zlib-ng/gzwrite.c ext/src/zlib-ng/infback.c ext/src/zlib-ng/inffast_tpl.h ext/src/zlib-ng/inflate.c ext/src/zlib-ng/inflate.h ext/src/zlib-ng/inftrees.c ext/src/zlib-ng/inftrees.h Copyright: 1995-2022, Mark Adler License: Zlib Files: ext/src/zlib-ng/adler32_fold.c ext/src/zlib-ng/adler32_fold.h Copyright: 2022, Adam Stylinski License: Zlib Files: ext/src/zlib-ng/arch/arm/Makefile.in Copyright: 1995-2022 Jean-loup Gailly, Mark Adler License: Zlib Files: ext/src/zlib-ng/arch/arm/adler32_neon.c Copyright: 2017 ARM Holdings Inc. 1995-2016 Mark Adler License: Zlib Files: ext/src/zlib-ng/arch/arm/compare256_neon.c Copyright: 2020-2022 Nathan Moinvaziri License: Zlib Files: ext/src/zlib-ng/arch/arm/crc32_acle.c Copyright: 2016 Yang Zhang 1995-2012 Mark Adler License: Zlib Files: ext/src/zlib-ng/arch/arm/slide_hash_armv6.c Copyright: 2023 Cameron Cawley License: Zlib Files: ext/src/zlib-ng/arch/arm/slide_hash_neon.c Copyright: 2017-2021 Mika T. 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License: Zlib Files: ext/src/zlib-ng/arch/s390/Makefile.in Copyright: 1995-2022 Jean-loup Gailly, Mark Adler License: Zlib Files: ext/src/zlib-ng/arch/x86/Makefile.in Copyright: 1995-2022 Jean-loup Gailly, Mark Adler License: Zlib Files: ext/src/zlib-ng/arch/x86/adler32_avx2.c ext/src/zlib-ng/arch/x86/adler32_avx512.c ext/src/zlib-ng/arch/x86/adler32_avx512_vnni.c ext/src/zlib-ng/arch/x86/adler32_sse42.c ext/src/zlib-ng/arch/x86/adler32_ssse3.c Copyright: 1995-2022 Mark Adler License: Zlib Files: ext/src/zlib-ng/arch/x86/adler32_avx2_p.h ext/src/zlib-ng/arch/x86/adler32_avx2_tpl.h ext/src/zlib-ng/arch/x86/adler32_avx512_tpl.h ext/src/zlib-ng/arch/x86/adler32_ssse3_p.h ext/src/zlib-ng/arch/x86/compare256_sse2.c Copyright: 2022 Adam Stylinski License: Zlib Files: ext/src/zlib-ng/arch/x86/compare256_avx2.c Copyright: 2017-2021 Mika T. Lindqvist License: Zlib Files: ext/src/zlib-ng/arch/x86/crc32_fold_pclmulqdq_tpl.h ext/src/zlib-ng/arch/x86/crc32_pclmulqdq.c ext/src/zlib-ng/arch/x86/crc32_pclmulqdq_tpl.h Copyright: 2016 Marian Beermann (support for initial value) 2013 Intel Corporation. License: Zlib Files: ext/src/zlib-ng/arch/x86/crc32_fold_vpclmulqdq_tpl.h ext/src/zlib-ng/arch/x86/crc32_vpclmulqdq.c Copyright: Wangyang Guo (wangyang.guo@intel.com) License: Zlib Files: ext/src/zlib-ng/arch/x86/slide_hash_avx2.c ext/src/zlib-ng/arch/x86/slide_hash_sse2.c Copyright: 2017 Intel Corporation License: Zlib Files: ext/src/zlib-ng/arch/x86/x86_features.c Copyright: 2013 Intel Corporation. License: Zlib Files: ext/src/zlib-ng/arch/x86/x86_features.h Copyright: 2013 Intel Corporation Jim Kukunas License: Zlib Files: ext/src/zlib-ng/cmake/detect-arch.c ext/src/zlib-ng/cmake/detect-arch.cmake ext/src/zlib-ng/cmake/detect-install-dirs.cmake Copyright: 2019-2021 Hans Kristian Rosbach License: Zlib Files: ext/src/zlib-ng/cmake/fallback-macros.cmake Copyright: 2021-2022 Nathan Moinvaziri License: Zlib Files: ext/src/zlib-ng/compare256.c ext/src/zlib-ng/compare256_rle.h ext/src/zlib-ng/crc32_fold.c ext/src/zlib-ng/crc32_fold.h Copyright: 2020-2022 Nathan Moinvaziri License: Zlib Files: ext/src/zlib-ng/cpu_features.c ext/src/zlib-ng/cpu_features.h ext/src/zlib-ng/functable.c ext/src/zlib-ng/functable.h Copyright: 2017 Hans Kristian Rosbach License: Zlib Files: ext/src/zlib-ng/deflate.h ext/src/zlib-ng/trees.c ext/src/zlib-ng/zutil.c Copyright: 1995-2021 Jean-loup Gailly License: Zlib Files: ext/src/zlib-ng/deflate_medium.c ext/src/zlib-ng/deflate_quick.c Copyright: 2013 Intel Corporation. License: Zlib Files: ext/src/zlib-ng/doc/rfc1950.txt Copyright: 1996 L. Peter Deutsch and Jean-Loup Gailly License: Zlib Files: ext/src/zlib-ng/doc/rfc1951.txt ext/src/zlib-ng/doc/rfc1952.txt Copyright: 1996 L. Peter Deutsch License: Zlib Files: ext/src/zlib-ng/insert_string_tpl.h Copyright: 2013 Intel Corporation. 1995-2013 Jean-loup Gailly and Mark Adler License: Zlib Files: ext/src/zlib-ng/match_tpl.h Copyright: 2014-2021 Konstantin Nosov 1995-2013 Jean-loup Gailly and Mark Adler License: Zlib Files: ext/src/zlib-ng/test/Makefile.in Copyright: 2015 Daniel Axtens, IBM Corporation 1995-2013 Jean-loup Gailly and Mark Adler License: Zlib Files: ext/src/zlib-ng/test/benchmarks/benchmark_adler32.cc ext/src/zlib-ng/test/benchmarks/benchmark_adler32_copy.cc Copyright: 2022 Nathan Moinvaziri, Adam Stylinski License: Zlib Files: ext/src/zlib-ng/test/benchmarks/benchmark_compare256.cc ext/src/zlib-ng/test/benchmarks/benchmark_compare256_rle.cc ext/src/zlib-ng/test/benchmarks/benchmark_crc32.cc ext/src/zlib-ng/test/benchmarks/benchmark_main.cc Copyright: 2020-2022 Nathan Moinvaziri License: Zlib Files: ext/src/zlib-ng/test/benchmarks/benchmark_slidehash.cc Copyright: 2022 Adam Stylinski, Nathan Moinvaziri License: Zlib Files: ext/src/zlib-ng/test/cmake/compress-and-verify.cmake ext/src/zlib-ng/test/cmake/run-and-compare.cmake ext/src/zlib-ng/test/cmake/run-and-redirect.cmake Copyright: 2021-2022 Nathan Moinvaziri License: Zlib Files: ext/src/zlib-ng/test/example.c ext/src/zlib-ng/test/minigzip.c ext/src/zlib-ng/test/fuzz/fuzzer_minigzip.c Copyright: 1995-2021 Jean-loup Gailly License: Zlib Files: ext/src/zlib-ng/test/infcover.c Copyright: 1995-2022 Mark Adler License: Zlib Files: ext/src/zlib-ng/test/minideflate.c ext/src/zlib-ng/test/test_compare256.cc ext/src/zlib-ng/test/test_compare256_rle.cc Copyright: 2020-2022 Nathan Moinvaziri License: Zlib Files: ext/src/zlib-ng/test/pigz/* Copyright: 2021-2022 Nathan Moinvaziri License: Zlib Files: ext/src/zlib-ng/test/test_adler32.cc ext/src/zlib-ng/test/test_crc32.cc Copyright: 2019-2021 IBM Corporation License: Zlib Files: ext/src/zlib-ng/tools/makecrct.c Copyright: 1995-2022 Mark Adler License: Zlib Files: ext/src/zlib-ng/tools/maketrees.c Copyright: 1995-2021 Jean-loup Gailly License: Zlib Files: ext/src/zlib-ng/uncompr.c Copyright: 1995-2016 Jean-loup Gailly, Mark Adler. License: Zlib Files: src/cmake/Modules/GetGitRevisionDescription.cmake src/cmake/Modules/GetGitRevisionDescription.cmake.in Copyright: Iowa State University 2009-2010 License: BSL-1.0 Files: src/common/adt/concurrent_dsu.cpp src/common/adt/iterator_range.hpp src/common/adt/lemiere_mod_reduce.hpp src/common/adt/pack.hpp src/common/alignment/* Copyright: 2023-2024 SPAdes team 2014-2023 Saint Petersburg State University License: GPL-2 Files: src/common/alignment/CMakeLists.txt src/common/alignment/edge_index.hpp src/common/alignment/kmer_mapper.hpp src/common/alignment/kmer_mapper_logger.hpp src/common/alignment/long_read_mapper.hpp src/common/alignment/long_read_storage.hpp src/common/alignment/sequence_mapper.hpp src/common/alignment/sequence_mapper_notifier.hpp src/common/alignment/pacbio/pac_index.hpp src/common/alignment/pacbio/pacbio_read_structures.hpp src/common/alignment/rna/* Copyright: 2023-2024 SPAdes team 2015-2022 Saint Petersburg State University 2011-2015 Saint Petersburg Academic University License: GPL-2 Files: src/common/assembly_graph/core/basic_graph_stats.hpp src/common/assembly_graph/core/construction_helper.hpp src/common/assembly_graph/core/debruijn_data.hpp src/common/assembly_graph/core/graph_core.hpp src/common/assembly_graph/core/id_distributor.hpp src/common/assembly_graph/core/kmer_iterator.hpp src/common/assembly_graph/graph_support/coverage_filling.hpp src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.hpp src/common/assembly_graph/graph_support/marks_and_locks.hpp src/common/assembly_graph/paths/* src/common/configs/aligner_config.hpp src/common/configs/distance_estimation.hpp src/common/hmm/* src/common/io/binary/* src/common/io/dataset_support/dataset_readers.cpp src/common/io/dataset_support/read_converter.cpp src/common/io/graph/* src/common/io/reads/async_read_stream.hpp src/common/io/reads/binary_converter.cpp src/common/io/reads/binary_streams.cpp src/common/io/reads/coverage_filtering_read_wrapper.hpp src/common/io/reads/edge_sequences_reader.hpp src/common/io/reads/file_read_flags.hpp src/common/io/reads/header_naming.hpp src/common/io/reads/io_helper.cpp src/common/io/reads/paired_readers.cpp src/common/io/sam/bam_parser.cpp src/common/io/sra/* src/common/io/utils/* src/common/kmer_index/* src/common/kmer_index/extension_index/kmer_extension_index_builder.hpp src/common/library/library_data.cpp src/common/library/library_data.hpp src/common/library/library_fwd.hpp src/common/modules/path_extend/gap_analyzer.cpp src/common/modules/path_extend/gap_analyzer.hpp src/common/modules/path_extend/loop_detector.cpp src/common/modules/path_extend/loop_traverser.cpp src/common/modules/path_extend/overlap_analysis.hpp src/common/modules/path_extend/overlap_remover.cpp src/common/modules/path_extend/overlap_remover.hpp src/common/modules/path_extend/path_deduplicator.hpp src/common/modules/path_extend/path_extender.hpp src/common/modules/path_extend/path_extenders.cpp src/common/modules/path_extend/pe_resolver.cpp src/common/modules/path_extend/pipeline/extenders_logic.hpp src/common/modules/path_extend/pipeline/launcher.cpp src/common/modules/path_extend/scaffolder2015/path_polisher.cpp src/common/modules/path_extend/scaffolder2015/path_polisher.hpp src/common/modules/simplification/complex_tip_clipper.hpp src/common/modules/simplification/superbubble_finder.hpp src/common/paired_info/concurrent_pair_info_buffer.hpp src/common/paired_info/distance_estimation_utils.cpp src/common/paired_info/distance_estimation_utils.hpp src/common/paired_info/histptr.hpp src/common/paired_info/paired_info_buffer.hpp src/common/paired_info/paired_info_helpers.hpp src/common/paired_info/paired_info_utils.cpp src/common/paired_info/paired_info_utils.hpp src/common/pipeline/graph_pack.cpp src/common/pipeline/graph_pack_helpers.cpp src/common/pipeline/sequence_mapper_gp_api.cpp src/common/sequence/genome_storage.hpp src/common/stages/read_conversion.cpp src/common/stages/read_conversion.hpp src/common/stages/ss_edge_split.cpp src/common/stages/ss_edge_split.hpp src/common/toolchain/* src/common/utils/filesystem/* src/common/utils/logger/* src/common/utils/memory_limit.cpp src/common/utils/version.cpp src/common/utils/perf/timetracer.hpp src/include/version.hpp src/projects/binspreader/* src/projects/cds_subgraphs/* src/projects/ionhammer/CMakeLists.txt src/projects/ionhammer/quality_metrics.h Copyright: 2023-2024 SPAdes team 2014-2023 Saint Petersburg State University License: GPL-2 Files: src/common/assembly_graph/paths/bidirectional_path.hpp src/common/assembly_graph/paths/mapping_path.hpp src/common/assembly_graph/paths/path_processor.hpp src/common/assembly_graph/paths/path_utils.hpp src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp src/common/kmer_index/extension_index/* src/common/kmer_index/kmer_mph/kmer_index.hpp src/common/kmer_index/kmer_mph/kmer_index_builder.hpp src/common/kmer_index/kmer_mph/kmer_splitters.hpp src/common/kmer_index/ph_map/key_with_hash.hpp src/common/kmer_index/ph_map/perfect_hash_map.hpp src/common/kmer_index/ph_map/storing_traits.hpp src/common/utils/filesystem/file_limit.hpp src/common/utils/filesystem/path_helper.cpp src/common/utils/filesystem/path_helper.hpp src/common/utils/logger/log_writers.hpp src/common/utils/logger/log_writers_thread.hpp src/common/utils/logger/logger.hpp Copyright: 2023-2024 SPAdes team 2015-2022 Saint Petersburg State University 2011-2015 Saint Petersburg Academic University License: GPL-2 Files: src/common/io/graph/gfa.cpp Copyright: 2023-2024 SPAdes team 2022 Anton Korobeynikov License: GPL-3+ Files: src/common/io/reads/mpmc_bounded.hpp Copyright: 2023-2024 SPAdes team 2015-2022 Saint Petersburg State University 2011-2014 Saint Petersburg Academic University License: BSD-2-clause Files: src/common/io/reads/parser.cpp src/common/io/reads/parser.hpp Copyright: 2023-2024 SPAdes team 2015-2022 Saint Petersburg State University 2011-2014 Saint Petersburg Academic University License: GPL-2+ Files: src/common/math/xmath.h Copyright: 2023-2024 SPAdes team 2015-2022 Saint Petersburg State University 2011-2014 Saint Petersburg Academic University License: BSD-3-clause Files: src/common/sequence/seq.hpp Copyright: 2023-2024 SPAdes team 2015-2022 Saint Petersburg State University 2011-2014 Saint Petersburg Academic University License: GPL-2+ Files: src/common/utils/md5.h Copyright: 2023-2024 SPAdes team 2015-2022 Saint Petersburg State University 2011-2014 Saint Petersburg Academic University License: NTP Files: src/projects/hammer/parallel_radix_sort.hpp Copyright: 2023-2024 SPAdes team 2015-2022 Saint Petersburg State University 2010 Takuya Akiba License: BSD-3-clause Files: src/projects/ionhammer/seqeval/* Copyright: 2023-2024 SPAdes team 2012-2013 Ion Torrent Systems, Inc. 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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 ABOVE 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. . Except as contained in this notice, the name(s) of the above copyright holders shall not be used in advertising or otherwise to promote the sale, use or other dealings in this Software without prior written authorization. License: Zlib 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. . 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