Rduckhts is distributed under GPL (>= 2), as declared in DESCRIPTION.

This package bundles third-party sources. Holders and licences below are taken
from the notices in the bundled files; paths are relative to the installed
package unless they start with a directory of the source tarball.

DuckHTS DuckDB extension
	Source: inst/duckhts_extension (files other than the third-party components below)
	Holder: DuckHTS Contributors (Copyright (c) 2026)
	License: MIT
	Reference: inst/duckhts_extension/LICENSE
	Note: inst/duckhts_extension/bcf_reader.c carries "Copyright (c) 2026 RBCFTools Authors" and
	inst/duckhts_extension/include/vep_parser.h records "Ported from RBCFTools"; both are part of
	the MIT-licensed extension sources.

riker insert-size semantics
	Source: inst/duckhts_extension/bam_insert_size_counts.c and insert_size_sql.c
	Holder: Fulcrum Genomics LLC (Copyright (c) 2026)
	License: MIT; permission notice reproduced in bam_insert_size_counts.c
	Note: Independently implemented semantics from riker v0.4.1, tag 40d5e326;
	no Rust code is bundled. Picard is context only, not the compatibility oracle.

HTSlib
	Source: inst/duckhts_extension/htslib
	Holders: Genome Research Ltd (files carry "Copyright (C) 2008-2026 Genome Research Ltd" and
	         similar year ranges); some files also name Broad Institute and Massachusetts
	         Institute of Technology, and Heng Li
	License: MIT/Expat for files outside cram/; Modified BSD 3-Clause for cram/
	Reference: inst/duckhts_extension/htslib/LICENSE
	Notes: HTSlib itself bundles or contains the following, each under the terms stated in its own file:
	- htscodecs (inst/duckhts_extension/htslib/htscodecs): Copyright Genome Research Limited, BSD
	  (see htslib/htscodecs/LICENSE.md). c_range_coder.h is Public Domain, derived from work by
	  Eugene Shelwien; rANS_byte.h and rANS_word.h are derived from Fabian Giesen's Public Domain
	  ryg_rans (CC0).
	- khash.h, kseq.h, klist.h, kfunc.h, kstring.h and kstring.c carry "Copyright ... Attractive
	  Chaos <attractor@live.co.uk>" (2008-2011) alongside Genome Research Ltd; other files (for
	  example vcf.h, tbx.c, faidx.c, errmod.c) carry Broad Institute and/or Massachusetts Institute
	  of Technology notices, and a file naming Heng Li as author (for example faidx.c, tbx.c,
	  vcf.h) keeps that attribution. The permission notice in each file governs it.
	- Some files in cram/ (misc.h, os.h, open_trace_file.c and open_trace_file.h) carry
	  "Copyright (c) 1993-2002 MEDICAL RESEARCH COUNCIL" (Modified BSD, stated in each file).
	- hts_time_funcs.h: time-zone code in the public domain ("clarified as of 1996-06-05 by
	  Arthur David Olson"); non-derived code is copyright as stated in the file.
	- os/lzma_stub.h: placed in the public domain, as stated in the file.
	- md5.c: Alexander Peslyak (Solar Designer), placed in the public domain; the file gives a
	  fallback licence permitting redistribution and modification.
	- os/rand.c: Copyright (c) 1993 Martin Birgmeier (terms stated in the file).
	- ref_cache/ sources: Copyright (C) 2025 Genome Research Ltd (MIT/Expat, stated in each file).
	- config.guess and config.sub: Copyright 1992-2025 Free Software Foundation, Inc.
	  (GNU General Public License version 3 or later, with the Autoconf configure-script exception
	  stated in each file).
	- m4/ macros: hts_check_compile_flags_needed.m4 (Copyright (c) 2008 Guido U. Draheim),
	  hts_hide_dynamic_syms.m4 (Copyright (C) 2018 Genome Research Ltd, MIT/Expat),
	  hts_prog_cc_warnings.m4 (AllPermissive), pkg.m4 (Copyright 2004 Scott James Remnant,
	  Copyright 2012-2015 Dan Nicholson); terms as stated in each file.
	The HTSlib sample programs under inst/duckhts_extension/htslib/samples are HTSlib project files
	covered by the HTSlib LICENSE.

bcftools filter expression engine
	Source: inst/duckhts_extension/bcftools_filter.c, inst/duckhts_extension/include/filter.h
	Holder: Genome Research Ltd (Copyright (C) 2013-2025 in bcftools_filter.c;
	        Copyright (C) 2013-2024 in filter.h)
	Author: Petr Danecek <pd3@sanger.ac.uk>
	License: MIT (permission notice reproduced in each file)
	Note: bcftools_filter.c is bcftools filter.c with local patches; see
	inst/duckhts_extension/include/bcftools_shim.h and bcftools_filter_config.h for the
	compatibility shims (no separate notice).

bcftools roh hidden Markov model
	Source: inst/duckhts_extension/roh_hmm.c, inst/duckhts_extension/include/roh_hmm.h
	Holder: Genome Research Ltd (Copyright (c) 2014-2026)
	Author: Petr Danecek <pd3@sanger.ac.uk>
	License: MIT; the upstream notice is reproduced below and at the head of roh_hmm.c.
	Note: roh_hmm.c ports the model of bcftools vcfroh.c and HMM.c (commit 6dbd8fef): emission
	probabilities, the precomputed transition matrices and genetic-map or constant-rate
	rescaling, Viterbi decoding, forward-backward posteriors and the RG segment rules.
	roh_udf.c and roh_sql.c are DuckHTS code (MIT) that call it.
	  The MIT License

	  Copyright (c) 2014-2026 Genome Research Ltd.

	  Author: Petr Danecek <pd3@sanger.ac.uk>

	  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.

BCFtools +score plugin functions
	Source: inst/duckhts_extension/score_udf.c. bcf_hdr_name2id_flexible() and
	        tsv_read_float_and_minus_log10() are ported from bcftools plugins/score.h and
	        marked as ports in the source.
	Holder: Giulio Genovese (Copyright (C) 2022-2025, score.h)
	License: MIT; the upstream notice is reproduced below.
	  The MIT License

	  Copyright (C) 2022-2025 Giulio Genovese

	  Author: Giulio Genovese <giulio.genovese@gmail.com>

	  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.

cgranges
	Source: inst/duckhts_extension/cgranges.c, inst/duckhts_extension/include/cgranges.h,
	        inst/duckhts_extension/include/khash.h
	Holders: Dana-Farber Cancer Institute (Copyright (c) 2019, cgranges.h);
	         Attractive Chaos <attractor@live.co.uk> (Copyright (c) 2008, 2009, 2011, khash.h)
	License: MIT ("The MIT License", notice in each header)
	Reference: inst/duckhts_extension/include/cgranges.h and inst/duckhts_extension/include/khash.h
	Note: cgranges.c has no notice of its own and is covered by cgranges.h; it is upstream
	cgranges (https://github.com/lh3/cgranges) with one local patch.

libBigWig
	Source: inst/duckhts_extension/libBigWig, inst/duckhts_extension/libbigwig_hfile_io.c
	Holder: Devon Ryan (Copyright (c) 2015)
	License: MIT
	Reference: inst/duckhts_extension/libBigWig/LICENSE
	Upstream commit: see inst/duckhts_extension/libBigWig/COMMIT
	Note: inst/extdata/libbigwig_test.bw is the upstream libBigWig test file.

VariantKey / RegionKey C API
	Source: inst/duckhts_extension/include/variantkey/{hex.h,variantkey.h,regionkey.h}
	Holders: GENOMICS plc (Copyright (c) 2017-2018 in each header; the upstream LICENSE names
	         2017-2019, 2023); Nicola Asuni - Tecnick.com (Copyright (c) 2017-2018, binsearch,
	         named in the upstream LICENSE)
	Author: Nicola Asuni <nicola.asuni@genomicsplc.com>
	License: MIT
	Reference: inst/duckhts_extension/include/variantkey/LICENSE

DuckDB C extension API headers
	Source: inst/duckhts_extension/duckdb_capi/duckdb.h and duckdb_extension.h
	Holder: Stichting DuckDB Foundation
	License: MIT
	Reference: inst/duckhts_extension/duckdb_capi/LICENSE (text reproduced below)
	Note: The headers are generated from DuckDB and carry no per-file copyright notice. They are
	DuckDB C API headers refreshed to v1.5.3 with one local patch
	(inst/patches/duckdb_capi_strict_prototypes.patch, C prototypes only). DuckDB's
	MIT licence applies to them; its text, taken from the DuckDB v1.5.3 LICENSE file, is:

	Copyright 2018-2025 Stichting DuckDB Foundation

	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.

Mosdepth test fixtures
	Source: inst/extdata/{bad.bed,big.bam,empty-tids.*,full-fragment-pairs.*,missing.bed,nanopore.*,overlapping-pairs.*,ovl.*,track.bed,unordered.bed}
	Authors: Brent Pedersen and mosdepth contributors
	License: MIT
	Reference: upstream mosdepth project LICENSE

Somalier-derived numerical methods
	Source: inst/duckhts_extension/somalier.c, inst/duckhts_extension/include/duckhts_somalier.h,
	        inst/duckhts_extension/include/bam_site_counts.h
	Author: Brent Pedersen and Somalier contributors
	License: MIT
	Reference: Somalier v0.3.4, commit ff58fdade8f4f8293d904f10e0a4a13f1fac808d
	Note: DuckHTS ports a defined computational subset; no Somalier Nim source or .somalier store is bundled.

GenBank test fixtures
	Source: inst/extdata/phix174.gb, inst/extdata/genbank_phase.gb, inst/extdata/genbank_gene_order.gb
	Authors: NCBI RefSeq record NC_001422.1 (Escherichia phage phiX174); the genbank_*.gb records are hand-written probes
	License: NCBI places no restrictions on the use or distribution of sequence records
	Reference: https://www.ncbi.nlm.nih.gov/nuccore/NC_001422.1
