git: 37be6965367e - main - New port: biology/seqan3: C++ header-only library for biological sequence analysis
Yuri Victorovich
yuri at FreeBSD.org
Wed May 12 01:21:41 UTC 2021
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=37be6965367eec49bc848623a2ad782d8f74471a
commit 37be6965367eec49bc848623a2ad782d8f74471a
Author: Yuri Victorovich <yuri at FreeBSD.org>
AuthorDate: 2021-05-12 01:20:55 +0000
Commit: Yuri Victorovich <yuri at FreeBSD.org>
CommitDate: 2021-05-12 01:21:38 +0000
New port: biology/seqan3: C++ header-only library for biological sequence analysis
---
biology/Makefile | 1 +
biology/seqan3/Makefile | 28 ++
biology/seqan3/distinfo | 5 +
biology/seqan3/pkg-descr | 9 +
biology/seqan3/pkg-plist | 673 +++++++++++++++++++++++++++++++++++++++++++++++
5 files changed, 716 insertions(+)
diff --git a/biology/Makefile b/biology/Makefile
index 358a2c77403e..e5bec235ca01 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -164,6 +164,7 @@
SUBDIR += seqan
SUBDIR += seqan-apps
SUBDIR += seqan1
+ SUBDIR += seqan3
SUBDIR += seqio
SUBDIR += seqkit
SUBDIR += seqtk
diff --git a/biology/seqan3/Makefile b/biology/seqan3/Makefile
new file mode 100644
index 000000000000..09dc6766ff68
--- /dev/null
+++ b/biology/seqan3/Makefile
@@ -0,0 +1,28 @@
+PORTNAME= seqan3
+DISTVERSION= 3.0.2-1195
+DISTVERSIONSUFFIX= -gee0dbcad
+CATEGORIES= biology devel math
+
+MAINTAINER= yuri at FreeBSD.org
+COMMENT= C++ header-only library for biological sequence analysis
+
+LICENSE= BSD3CLAUSE
+LICENSE_FILE= ${WRKSRC}/LICENSE.md
+
+HPP_DEPENDS= cereal>0:devel/cereal \
+ coin-or-lemon>0:math/lemon \
+ range-v3>0:devel/range-v3
+BUILD_DEPENDS= ${HPP_DEPENDS}
+
+USES= cmake localbase
+
+USE_GITHUB= yes
+GH_ACCOUNT= seqan
+GH_TUPLE= xxsds:sdsl-lite:9a0d567:sdsl_lite/submodules/sdsl-lite
+
+NO_ARCH= yes
+
+post-install:
+ @${RM} -r ${STAGEDIR}${DOCSDIR}
+
+.include <bsd.port.mk>
diff --git a/biology/seqan3/distinfo b/biology/seqan3/distinfo
new file mode 100644
index 000000000000..408948c836d6
--- /dev/null
+++ b/biology/seqan3/distinfo
@@ -0,0 +1,5 @@
+TIMESTAMP = 1620779602
+SHA256 (seqan-seqan3-3.0.2-1195-gee0dbcad_GH0.tar.gz) = 6a838f97be0c850e46141fa9afa081f76ce9196e64e395ce8928da7e7fb73cd9
+SIZE (seqan-seqan3-3.0.2-1195-gee0dbcad_GH0.tar.gz) = 1456878
+SHA256 (xxsds-sdsl-lite-9a0d567_GH0.tar.gz) = 1727ec6897535a493b99ff36a6d19d8205964be2b2a027ba547fc77ab7dbd74e
+SIZE (xxsds-sdsl-lite-9a0d567_GH0.tar.gz) = 1156974
diff --git a/biology/seqan3/pkg-descr b/biology/seqan3/pkg-descr
new file mode 100644
index 000000000000..8cb4595b3673
--- /dev/null
+++ b/biology/seqan3/pkg-descr
@@ -0,0 +1,9 @@
+SeqAn3 is the new version of the popular SeqAn template library for the analysis
+of biological sequences. It enables the rapid development of high-performance
+solutions by providing generic algorithms and data structures for:
+* sequence representation and transformation
+* full-text indexing and efficient search
+* sequence alignment
+* input/output of common file formats
+
+WWW: https://github.com/seqan/seqan3
diff --git a/biology/seqan3/pkg-plist b/biology/seqan3/pkg-plist
new file mode 100644
index 000000000000..675c0f36cead
--- /dev/null
+++ b/biology/seqan3/pkg-plist
@@ -0,0 +1,673 @@
+include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp
+include/seqan3/alignment/aligned_sequence/all.hpp
+include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp
+include/seqan3/alignment/all.hpp
+include/seqan3/alignment/band/all.hpp
+include/seqan3/alignment/band/static_band.hpp
+include/seqan3/alignment/configuration/align_config_band.hpp
+include/seqan3/alignment/configuration/align_config_debug.hpp
+include/seqan3/alignment/configuration/align_config_edit.hpp
+include/seqan3/alignment/configuration/align_config_gap_cost_affine.hpp
+include/seqan3/alignment/configuration/align_config_method.hpp
+include/seqan3/alignment/configuration/align_config_min_score.hpp
+include/seqan3/alignment/configuration/align_config_on_result.hpp
+include/seqan3/alignment/configuration/align_config_output.hpp
+include/seqan3/alignment/configuration/align_config_parallel.hpp
+include/seqan3/alignment/configuration/align_config_result_type.hpp
+include/seqan3/alignment/configuration/align_config_score_type.hpp
+include/seqan3/alignment/configuration/align_config_scoring_scheme.hpp
+include/seqan3/alignment/configuration/align_config_vectorised.hpp
+include/seqan3/alignment/configuration/all.hpp
+include/seqan3/alignment/configuration/detail.hpp
+include/seqan3/alignment/decorator/gap_decorator.hpp
+include/seqan3/alignment/detail/pairwise_alignment_concept.hpp
+include/seqan3/alignment/exception.hpp
+include/seqan3/alignment/matrix/alignment_coordinate.hpp
+include/seqan3/alignment/matrix/alignment_optimum.hpp
+include/seqan3/alignment/matrix/all.hpp
+include/seqan3/alignment/matrix/debug_matrix.hpp
+include/seqan3/alignment/matrix/detail/advanceable_alignment_coordinate.hpp
+include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp
+include/seqan3/alignment/matrix/detail/aligned_sequence_builder.hpp
+include/seqan3/alignment/matrix/detail/alignment_matrix_column_major_range_base.hpp
+include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column.hpp
+include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_banded.hpp
+include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp
+include/seqan3/alignment/matrix/detail/alignment_score_matrix_proxy.hpp
+include/seqan3/alignment/matrix/detail/alignment_trace_matrix_base.hpp
+include/seqan3/alignment/matrix/detail/alignment_trace_matrix_full.hpp
+include/seqan3/alignment/matrix/detail/alignment_trace_matrix_full_banded.hpp
+include/seqan3/alignment/matrix/detail/alignment_trace_matrix_proxy.hpp
+include/seqan3/alignment/matrix/detail/all.hpp
+include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp
+include/seqan3/alignment/matrix/detail/coordinate_matrix.hpp
+include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp
+include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp
+include/seqan3/alignment/matrix/detail/trace_iterator.hpp
+include/seqan3/alignment/matrix/detail/trace_iterator_banded.hpp
+include/seqan3/alignment/matrix/detail/trace_iterator_base.hpp
+include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp
+include/seqan3/alignment/matrix/detail/two_dimensional_matrix.hpp
+include/seqan3/alignment/matrix/detail/two_dimensional_matrix_iterator_base.hpp
+include/seqan3/alignment/matrix/detail/two_dimensional_matrix_iterator_concept.hpp
+include/seqan3/alignment/matrix/edit_distance_score_matrix_full.hpp
+include/seqan3/alignment/matrix/edit_distance_trace_matrix_full.hpp
+include/seqan3/alignment/matrix/matrix_concept.hpp
+include/seqan3/alignment/matrix/row_wise_matrix.hpp
+include/seqan3/alignment/matrix/trace_directions.hpp
+include/seqan3/alignment/pairwise/align_pairwise.hpp
+include/seqan3/alignment/pairwise/align_result_selector.hpp
+include/seqan3/alignment/pairwise/alignment_algorithm.hpp
+include/seqan3/alignment/pairwise/alignment_configurator.hpp
+include/seqan3/alignment/pairwise/alignment_result.hpp
+include/seqan3/alignment/pairwise/all.hpp
+include/seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp
+include/seqan3/alignment/pairwise/detail/concept.hpp
+include/seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm.hpp
+include/seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm_banded.hpp
+include/seqan3/alignment/pairwise/detail/policy_affine_gap_recursion.hpp
+include/seqan3/alignment/pairwise/detail/policy_affine_gap_recursion_banded.hpp
+include/seqan3/alignment/pairwise/detail/policy_affine_gap_with_trace_recursion.hpp
+include/seqan3/alignment/pairwise/detail/policy_affine_gap_with_trace_recursion_banded.hpp
+include/seqan3/alignment/pairwise/detail/policy_alignment_matrix.hpp
+include/seqan3/alignment/pairwise/detail/policy_alignment_result_builder.hpp
+include/seqan3/alignment/pairwise/detail/policy_optimum_tracker.hpp
+include/seqan3/alignment/pairwise/detail/policy_optimum_tracker_simd.hpp
+include/seqan3/alignment/pairwise/detail/policy_scoring_scheme.hpp
+include/seqan3/alignment/pairwise/detail/type_traits.hpp
+include/seqan3/alignment/pairwise/edit_distance_algorithm.hpp
+include/seqan3/alignment/pairwise/edit_distance_fwd.hpp
+include/seqan3/alignment/pairwise/edit_distance_unbanded.hpp
+include/seqan3/alignment/pairwise/policy/affine_gap_init_policy.hpp
+include/seqan3/alignment/pairwise/policy/affine_gap_policy.hpp
+include/seqan3/alignment/pairwise/policy/alignment_matrix_policy.hpp
+include/seqan3/alignment/pairwise/policy/all.hpp
+include/seqan3/alignment/pairwise/policy/find_optimum_policy.hpp
+include/seqan3/alignment/pairwise/policy/scoring_scheme_policy.hpp
+include/seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp
+include/seqan3/alignment/pairwise/policy/simd_find_optimum_policy.hpp
+include/seqan3/alignment/scoring/all.hpp
+include/seqan3/alignment/scoring/aminoacid_scoring_scheme.hpp
+include/seqan3/alignment/scoring/detail/simd_match_mismatch_scoring_scheme.hpp
+include/seqan3/alignment/scoring/detail/simd_matrix_scoring_scheme.hpp
+include/seqan3/alignment/scoring/gap_scheme.hpp
+include/seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp
+include/seqan3/alignment/scoring/scoring_scheme_base.hpp
+include/seqan3/alignment/scoring/scoring_scheme_concept.hpp
+include/seqan3/alphabet/adaptation/all.hpp
+include/seqan3/alphabet/adaptation/char.hpp
+include/seqan3/alphabet/adaptation/uint.hpp
+include/seqan3/alphabet/all.hpp
+include/seqan3/alphabet/alphabet_base.hpp
+include/seqan3/alphabet/aminoacid/aa10li.hpp
+include/seqan3/alphabet/aminoacid/aa10murphy.hpp
+include/seqan3/alphabet/aminoacid/aa20.hpp
+include/seqan3/alphabet/aminoacid/aa27.hpp
+include/seqan3/alphabet/aminoacid/all.hpp
+include/seqan3/alphabet/aminoacid/aminoacid_base.hpp
+include/seqan3/alphabet/aminoacid/concept.hpp
+include/seqan3/alphabet/aminoacid/translation.hpp
+include/seqan3/alphabet/aminoacid/translation_details.hpp
+include/seqan3/alphabet/aminoacid/translation_genetic_code.hpp
+include/seqan3/alphabet/cigar/all.hpp
+include/seqan3/alphabet/cigar/cigar.hpp
+include/seqan3/alphabet/cigar/cigar_op.hpp
+include/seqan3/alphabet/cigar/exposition_only/cigar_operation.hpp
+include/seqan3/alphabet/composite/all.hpp
+include/seqan3/alphabet/composite/alphabet_tuple_base.hpp
+include/seqan3/alphabet/composite/alphabet_variant.hpp
+include/seqan3/alphabet/composite/detail.hpp
+include/seqan3/alphabet/composite/semialphabet_any.hpp
+include/seqan3/alphabet/concept.hpp
+include/seqan3/alphabet/container/bitpacked_sequence.hpp
+include/seqan3/alphabet/container/concatenated_sequences.hpp
+include/seqan3/alphabet/detail/alphabet_proxy.hpp
+include/seqan3/alphabet/detail/convert.hpp
+include/seqan3/alphabet/exception.hpp
+include/seqan3/alphabet/gap/all.hpp
+include/seqan3/alphabet/gap/gap.hpp
+include/seqan3/alphabet/gap/gapped.hpp
+include/seqan3/alphabet/hash.hpp
+include/seqan3/alphabet/mask/all.hpp
+include/seqan3/alphabet/mask/mask.hpp
+include/seqan3/alphabet/mask/masked.hpp
+include/seqan3/alphabet/nucleotide/all.hpp
+include/seqan3/alphabet/nucleotide/concept.hpp
+include/seqan3/alphabet/nucleotide/dna15.hpp
+include/seqan3/alphabet/nucleotide/dna16sam.hpp
+include/seqan3/alphabet/nucleotide/dna3bs.hpp
+include/seqan3/alphabet/nucleotide/dna4.hpp
+include/seqan3/alphabet/nucleotide/dna5.hpp
+include/seqan3/alphabet/nucleotide/nucleotide_base.hpp
+include/seqan3/alphabet/nucleotide/rna15.hpp
+include/seqan3/alphabet/nucleotide/rna4.hpp
+include/seqan3/alphabet/nucleotide/rna5.hpp
+include/seqan3/alphabet/nucleotide/sam_dna16.hpp
+include/seqan3/alphabet/quality/aliases.hpp
+include/seqan3/alphabet/quality/all.hpp
+include/seqan3/alphabet/quality/concept.hpp
+include/seqan3/alphabet/quality/phred42.hpp
+include/seqan3/alphabet/quality/phred63.hpp
+include/seqan3/alphabet/quality/phred68legacy.hpp
+include/seqan3/alphabet/quality/phred68solexa.hpp
+include/seqan3/alphabet/quality/phred94.hpp
+include/seqan3/alphabet/quality/phred_base.hpp
+include/seqan3/alphabet/quality/qualified.hpp
+include/seqan3/alphabet/quality/quality_base.hpp
+include/seqan3/alphabet/range/hash.hpp
+include/seqan3/alphabet/range/sequence.hpp
+include/seqan3/alphabet/structure/all.hpp
+include/seqan3/alphabet/structure/concept.hpp
+include/seqan3/alphabet/structure/dot_bracket3.hpp
+include/seqan3/alphabet/structure/dssp9.hpp
+include/seqan3/alphabet/structure/structured_aa.hpp
+include/seqan3/alphabet/structure/structured_rna.hpp
+include/seqan3/alphabet/structure/wuss.hpp
+include/seqan3/alphabet/views/all.hpp
+include/seqan3/alphabet/views/char_to.hpp
+include/seqan3/alphabet/views/complement.hpp
+include/seqan3/alphabet/views/rank_to.hpp
+include/seqan3/alphabet/views/to_char.hpp
+include/seqan3/alphabet/views/to_rank.hpp
+include/seqan3/alphabet/views/translate.hpp
+include/seqan3/alphabet/views/translate_join.hpp
+include/seqan3/alphabet/views/trim_quality.hpp
+include/seqan3/argument_parser/all.hpp
+include/seqan3/argument_parser/argument_parser.hpp
+include/seqan3/argument_parser/auxiliary.hpp
+include/seqan3/argument_parser/detail/format_base.hpp
+include/seqan3/argument_parser/detail/format_help.hpp
+include/seqan3/argument_parser/detail/format_html.hpp
+include/seqan3/argument_parser/detail/format_man.hpp
+include/seqan3/argument_parser/detail/format_parse.hpp
+include/seqan3/argument_parser/detail/terminal.hpp
+include/seqan3/argument_parser/detail/version_check.hpp
+include/seqan3/argument_parser/exceptions.hpp
+include/seqan3/argument_parser/validators.hpp
+include/seqan3/contrib/charconv/LICENSE.TXT
+include/seqan3/contrib/charconv/charconv
+include/seqan3/contrib/charconv/charconv.cpp
+include/seqan3/contrib/charconv/charconv_pre.hpp
+include/seqan3/contrib/parallel/buffer_queue.hpp
+include/seqan3/contrib/parallel/serialised_resource_pool.hpp
+include/seqan3/contrib/parallel/suspendable_queue.hpp
+include/seqan3/contrib/span/span
+include/seqan3/contrib/stream/bgzf_istream.hpp
+include/seqan3/contrib/stream/bgzf_ostream.hpp
+include/seqan3/contrib/stream/bgzf_stream_util.hpp
+include/seqan3/contrib/stream/bz2_istream.hpp
+include/seqan3/contrib/stream/bz2_ostream.hpp
+include/seqan3/contrib/stream/gz_istream.hpp
+include/seqan3/contrib/stream/gz_ostream.hpp
+include/seqan3/core/add_enum_bitwise_operators.hpp
+include/seqan3/core/algorithm/algorithm_result_generator_range.hpp
+include/seqan3/core/algorithm/all.hpp
+include/seqan3/core/algorithm/bound.hpp
+include/seqan3/core/algorithm/concept.hpp
+include/seqan3/core/algorithm/configuration.hpp
+include/seqan3/core/algorithm/configuration_element_debug_mode.hpp
+include/seqan3/core/algorithm/configuration_element_parallel_mode.hpp
+include/seqan3/core/algorithm/configuration_utility.hpp
+include/seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp
+include/seqan3/core/algorithm/detail/all.hpp
+include/seqan3/core/algorithm/detail/execution_handler_parallel.hpp
+include/seqan3/core/algorithm/detail/execution_handler_sequential.hpp
+include/seqan3/core/algorithm/pipeable_config_element.hpp
+include/seqan3/core/all.hpp
+include/seqan3/core/bit_manipulation.hpp
+include/seqan3/core/char_operations/all.hpp
+include/seqan3/core/char_operations/predicate.hpp
+include/seqan3/core/char_operations/predicate_detail.hpp
+include/seqan3/core/char_operations/pretty_print.hpp
+include/seqan3/core/char_operations/transform.hpp
+include/seqan3/core/common_tuple.hpp
+include/seqan3/core/concept/all.hpp
+include/seqan3/core/concept/cereal.hpp
+include/seqan3/core/concept/core_language.hpp
+include/seqan3/core/concept/tuple.hpp
+include/seqan3/core/configuration/all.hpp
+include/seqan3/core/configuration/configuration.hpp
+include/seqan3/core/configuration/detail/all.hpp
+include/seqan3/core/configuration/detail/concept.hpp
+include/seqan3/core/configuration/detail/configuration_element_debug_mode.hpp
+include/seqan3/core/configuration/detail/configuration_element_parallel_mode.hpp
+include/seqan3/core/configuration/detail/configuration_utility.hpp
+include/seqan3/core/debug_stream.hpp
+include/seqan3/core/debug_stream/detail/to_string.hpp
+include/seqan3/core/detail/all.hpp
+include/seqan3/core/detail/customisation_point.hpp
+include/seqan3/core/detail/debug_stream_alphabet.hpp
+include/seqan3/core/detail/debug_stream_byte.hpp
+include/seqan3/core/detail/debug_stream_optional.hpp
+include/seqan3/core/detail/debug_stream_range.hpp
+include/seqan3/core/detail/debug_stream_tuple.hpp
+include/seqan3/core/detail/debug_stream_type.hpp
+include/seqan3/core/detail/debug_stream_variant.hpp
+include/seqan3/core/detail/deferred_crtp_base.hpp
+include/seqan3/core/detail/empty_type.hpp
+include/seqan3/core/detail/endian.hpp
+include/seqan3/core/detail/int_types.hpp
+include/seqan3/core/detail/is_class_template_declarable.hpp
+include/seqan3/core/detail/iterator_traits.hpp
+include/seqan3/core/detail/pack_algorithm.hpp
+include/seqan3/core/detail/persist_view.hpp
+include/seqan3/core/detail/strong_type.hpp
+include/seqan3/core/detail/template_inspection.hpp
+include/seqan3/core/detail/test_accessor.hpp
+include/seqan3/core/detail/to_string.hpp
+include/seqan3/core/detail/transfer_type_modifier_onto.hpp
+include/seqan3/core/detail/type_inspection.hpp
+include/seqan3/core/math.hpp
+include/seqan3/core/parallel/all.hpp
+include/seqan3/core/parallel/detail/latch.hpp
+include/seqan3/core/parallel/detail/reader_writer_manager.hpp
+include/seqan3/core/parallel/detail/spin_delay.hpp
+include/seqan3/core/parallel/execution.hpp
+include/seqan3/core/platform.hpp
+include/seqan3/core/pod_tuple.hpp
+include/seqan3/core/range/detail/inherited_iterator_base.hpp
+include/seqan3/core/range/detail/misc.hpp
+include/seqan3/core/range/detail/random_access_iterator.hpp
+include/seqan3/core/range/type_traits.hpp
+include/seqan3/core/semiregular_box.hpp
+include/seqan3/core/simd/all.hpp
+include/seqan3/core/simd/concept.hpp
+include/seqan3/core/simd/debug_stream_simd.hpp
+include/seqan3/core/simd/detail/builtin_simd.hpp
+include/seqan3/core/simd/detail/builtin_simd_intrinsics.hpp
+include/seqan3/core/simd/detail/default_simd_backend.hpp
+include/seqan3/core/simd/detail/default_simd_length.hpp
+include/seqan3/core/simd/detail/simd_algorithm_avx2.hpp
+include/seqan3/core/simd/detail/simd_algorithm_avx512.hpp
+include/seqan3/core/simd/detail/simd_algorithm_sse4.hpp
+include/seqan3/core/simd/simd.hpp
+include/seqan3/core/simd/simd_algorithm.hpp
+include/seqan3/core/simd/simd_traits.hpp
+include/seqan3/core/simd/view_iota_simd.hpp
+include/seqan3/core/simd/view_to_simd.hpp
+include/seqan3/core/tuple/common_tuple.hpp
+include/seqan3/core/tuple_utility.hpp
+include/seqan3/core/type_list/all.hpp
+include/seqan3/core/type_list/traits.hpp
+include/seqan3/core/type_list/type_list.hpp
+include/seqan3/core/type_traits/all.hpp
+include/seqan3/core/type_traits/basic.hpp
+include/seqan3/core/type_traits/concept.hpp
+include/seqan3/core/type_traits/deferred_crtp_base.hpp
+include/seqan3/core/type_traits/function.hpp
+include/seqan3/core/type_traits/iterator.hpp
+include/seqan3/core/type_traits/lazy.hpp
+include/seqan3/core/type_traits/pack.hpp
+include/seqan3/core/type_traits/pre.hpp
+include/seqan3/core/type_traits/range.hpp
+include/seqan3/core/type_traits/template_inspection.hpp
+include/seqan3/core/type_traits/transformation_trait_or.hpp
+include/seqan3/io/alignment_file/all.hpp
+include/seqan3/io/alignment_file/detail.hpp
+include/seqan3/io/alignment_file/format_bam.hpp
+include/seqan3/io/alignment_file/format_sam.hpp
+include/seqan3/io/alignment_file/format_sam_base.hpp
+include/seqan3/io/alignment_file/header.hpp
+include/seqan3/io/alignment_file/input.hpp
+include/seqan3/io/alignment_file/input_format_concept.hpp
+include/seqan3/io/alignment_file/input_options.hpp
+include/seqan3/io/alignment_file/misc.hpp
+include/seqan3/io/alignment_file/output.hpp
+include/seqan3/io/alignment_file/output_format_concept.hpp
+include/seqan3/io/alignment_file/output_options.hpp
+include/seqan3/io/alignment_file/sam_tag_dictionary.hpp
+include/seqan3/io/all.hpp
+include/seqan3/io/detail/ignore_output_iterator.hpp
+include/seqan3/io/detail/in_file_iterator.hpp
+include/seqan3/io/detail/istreambuf_view.hpp
+include/seqan3/io/detail/magic_header.hpp
+include/seqan3/io/detail/misc.hpp
+include/seqan3/io/detail/misc_input.hpp
+include/seqan3/io/detail/misc_output.hpp
+include/seqan3/io/detail/out_file_iterator.hpp
+include/seqan3/io/detail/record.hpp
+include/seqan3/io/detail/record_like.hpp
+include/seqan3/io/detail/safe_filesystem_entry.hpp
+include/seqan3/io/detail/take_exactly_view.hpp
+include/seqan3/io/detail/take_line_view.hpp
+include/seqan3/io/detail/take_until_view.hpp
+include/seqan3/io/detail/take_view.hpp
+include/seqan3/io/exception.hpp
+include/seqan3/io/record.hpp
+include/seqan3/io/sam_file/all.hpp
+include/seqan3/io/sam_file/detail/cigar.hpp
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