File all.hpp: This header will be removed in 3.1.0; The contained functionality has been replaced by the seqan3::align_cfg::band_fixed_size configuration.
File all.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/all.hpp> instead.
File all.hpp: This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/utility/char_operations/all.hpp> instead.
File all.hpp: This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/utility/parallel/all.hpp> instead.
File all.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please #include <seqan3/utility/type_traits/all.hpp> instead.
File all.hpp: This header is deprecated and will be removed in SeqAn-3.1.0;. Please #include <seqan3/utility/type_list/all.hpp> and <seqan3/utility/type_pack/all.hpp> instead.
File all.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/all.hpp instead.
File basic.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please #include <seqan3/utility/type_traits/basic.hpp> instead.
Class bi_fm_index_cursor_specialisation: Use seqan3::detail::template_specialisation_of<t, seqan3::bi_fm_index_cursor> instead.
Class bi_fm_index_specialisation: Use seqan3::detail::template_specialisation_of<typename t::cursor_type, seqan3::bi_fm_index_cursor> instead.
File bit_manipulation.hpp: This header will be removed in 3.1.0; Please #include <seqan3/utility/detail/bit_manipulation.hpp> instead.
File bound.hpp: This header will be removed in 3.1.0; The contained functionality has been replaced by the seqan3::align_cfg::band_fixed_size configuration.
File builtin_simd.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/detail/builtin_simd.hpp instead.
File builtin_simd_intrinsics.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/detail/builtin_simd_intrinsics.hpp instead.
File char_to.hpp: This header will be removed in 3.1. Please use seqan3/alphabet/views/char_to.hpp instead.
File chunk.hpp: This header will be removed in 3.1. Please use seqan3/utility/views/chunk.hpp instead.
File cigar_op.hpp: This header will be removed in 3.1.0; Please #include <seqan3/alphabet/cigar/cigar.hpp> instead.
File common_tuple.hpp: This header will be removed in 3.1.0; Please #include <seqan3/core/tuple/common_tuple.hpp> instead.
File complement.hpp: This header will be removed in 3.1. Please use seqan3/alphabet/views/complement.hpp instead.
File concept.hpp: This header will be removed in 3.1.0; Please #include <seqan3/core/configuration/detail/concept.hpp> instead.
File concept.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please #include <seqan3/utility/type_traits/concept.hpp> instead.
File concept.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/concept.hpp instead.
File configuration.hpp: This header will be removed in 3.1.0; Please #include <seqan3/core/configuration/configuration.hpp> instead.
File configuration_element_debug_mode.hpp: This header will be removed in 3.1.0; Please #include <seqan3/core/configuration/detail/configuration_element_debug_mode.hpp> instead.
File configuration_element_parallel_mode.hpp: This header will be removed in 3.1.0; Please #include <seqan3/core/configuration/detail/configuration_element_parallel_mode.hpp> instead.
File configuration_utility.hpp: This header will be removed in 3.1.0; Please #include <seqan3/core/configuration/detail/configuration_utility.hpp> instead.
File convert.hpp: This header will be removed in 3.1. Please use seqan3/utility/views/convert.hpp instead.
File core_language.hpp: This header will be removed in 3.1.0; Please #include <seqan3/utility/detail/exposition_only_concept.hpp> instead.
File debug_stream_simd.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/detail/debug_stream_simd.hpp instead.
File deep.hpp: This header will be removed in 3.1. Please use seqan3/utility/views/deep.hpp instead.
File default_simd_backend.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/detail/default_simd_backend.hpp instead.
File default_simd_length.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/detail/default_simd_length.hpp instead.
File deferred_crtp_base.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please #include <seqan3/core/detail/deferred_crtp_base.hpp> instead.
File detail.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/detail/cigar.hpp> instead.
File endian.hpp: This header is deprecated and will be removed in SeqAn-3.1.0;. Please use std::endian and #include <seqan3/std/bit> instead.
File enforce_random_access.hpp: This header will be removed in 3.1. Please use seqan3/utility/views/enforce_random_access.hpp instead.
Class fm_index_cursor_specialisation: Use seqan3::detail::template_specialisation_of<t, seqan3::fm_index_cursor> instead.
Class fm_index_specialisation: Use seqan3::detail::template_specialisation_of<typename t::cursor_type, seqan3::fm_index_cursor> instead.
File format_bam.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/format_bam.hpp> instead.
File format_sam.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/format_sam.hpp> instead.
File format_sam_base.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/detail/format_sam_base.hpp> instead.
File function.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please #include <seqan3/utility/type_traits/function_traits.hpp> or <seqan3/utility/detail/multi_invocable.hpp> instead.
File header.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/header.hpp> instead.
File input.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/input.hpp> instead.
File input_format_concept.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/input_format_concept.hpp> instead.
File input_options.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/input_options.hpp> instead.
File int_types.hpp: This header is deprecated and will be removed in SeqAn-3.1.0;. Please #include <seqan3/utility/detail/integer_traits.hpp> instead.
File iterator.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please #include <seqan3/core/detail/iterator_traits.hpp> instead.
File latch.hpp: This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/utility/parallel/detail/latch.hpp> instead.
File lazy.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please #include <seqan3/utility/type_traits/lazy_conditional.hpp> or <seqan3/core/detail/is_class_template_declarable.hpp> instead.
File math.hpp: This header will be removed in 3.1. Please use seqan3/utility/math.hpp instead.
File misc.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/sam_flag.hpp> instead.
File output.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/output.hpp> instead.
File output_format_concept.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/output_format_concept.hpp> instead.
File output_options.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/output_options.hpp> instead.
File pack.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please use seqan3::pack_traits::contains in <seqan3/core/type_list/traits.hpp> instead.
File phred68legacy.hpp: This header will be removed in 3.1.0; Please #include <seqan3/alphabet/quality/phred68solexa.hpp> instead.
File pod_tuple.hpp: This header will be removed in 3.1.0; Please #include <seqan3/utility/tuple/pod_tuple.hpp> instead.
File pre.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please #include <seqan3/utility/type_traits/pre.hpp> instead.
File predicate.hpp: This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/utility/char_operations/predicate.hpp> instead.
File predicate_detail.hpp: This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/utility/char_operations/predicate_detail.hpp> instead.
File pretty_print.hpp: This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/utility/char_operations/pretty_print.hpp> instead.
File quality_base.hpp: This header will be removed in 3.1.0; Please #include <seqan3/alphabet/quality/phred_base.hpp> instead.
File range.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please #include <seqan3/core/range/type_traits.hpp> instead.
Class range_compatible: This concept is deprecated and will be removed in SeqAn-3.1.
File rank_to.hpp: This header will be removed in 3.1. Please use seqan3/alphabet/views/rank_to.hpp instead.
File reader_writer_manager.hpp: This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/utility/parallel/detail/reader_writer_manager.hpp> instead.
File repeat.hpp: This header will be removed in 3.1. Please use seqan3/utility/views/repeat.hpp instead.
File repeat_n.hpp: This header will be removed in 3.1. Please use seqan3/utility/views/repeat_n.hpp instead.
File sam_dna16.hpp: This header will be removed in 3.1.0; Please #include seqan3/alphabet/nucleotide/dna16sam.hpp instead.
File sam_tag_dictionary.hpp: This header will be removed in 3.1.0; Please #include <seqan3/io/sam_file/sam_tag_dictionary.hpp> instead.
Member seqan3::ADVANCED: Use seqan3::option_spec::advanced instead.
Class seqan3::alignment_file_header< ref_ids_type >: Use seqan3::sam_file_header instead.
Class seqan3::alignment_file_input< traits_type_, selected_field_ids_, valid_formats_ >: Use seqan3::sam_file_input instead.
Member seqan3::alignment_file_input_default_traits: Use seqan3::sam_file_input_default_traits instead.
Member seqan3::alignment_file_input_format: Use seqan3::sam_file_input_format instead.
Member seqan3::alignment_file_input_options: Use seqan3::sam_file_input_options instead.
Class seqan3::alignment_file_output< selected_field_ids_, valid_formats_, ref_ids_type >: Use seqan3::sam_file_output instead.
Member seqan3::alignment_file_output_format: Use seqan3::sam_file_output_format instead.
Member seqan3::alignment_file_output_options: Use seqan3::sam_file_output_options instead.
Member seqan3::argument_parser::argument_parser (std::string const app_name, int const argc, char const *const *const argv, bool version_updates, std::vector< std::string > subcommands={}): Please use seqan3::update_notifications::on or seqan3::update_notifications::off for version_updates.
Member seqan3::CANONICAL: Use seqan3::genetic_code::canonical instead.
Member seqan3::cigar_op: Please use seqan3::cigar::operation instead.
Member seqan3::concatenated_sequences< inner_type, data_delimiters_type >::data () const: Use raw_data() instead.
Member seqan3::concatenated_sequences< inner_type, data_delimiters_type >::data (): Use raw_data() instead.
Class seqan3::const_reference< t >: If t models std::ranges::range use std::ranges::range_reference_t<t const> instead or if t models std::input_iterator use std::iter_reference_t<t const> instead.
Member seqan3::const_reference_t: If t models std::ranges::range use std::ranges::range_reference_t<t const> instead or if t models std::input_iterator use std::iter_reference_t<t const> instead.
Member seqan3::DEFAULT: Use seqan3::option_spec::standard instead.
Class seqan3::difference_type< t >: If t models std::ranges::range use std::ranges::range_difference_t instead or if t models std::input_iterator use std::iter_difference_t instead.
Member seqan3::difference_type_t: If t models std::ranges::range use std::ranges::range_difference_t instead or if t models std::input_iterator use std::iter_difference_t instead.
Class seqan3::gap_open_score< score_type >: This type is deprecated and will be removed in SeqAn3.1.
Class seqan3::gap_scheme< score_t >: This type is deprecated and will be removed in SeqAn3.1.
Class seqan3::gap_score< score_type >: This type is deprecated and will be removed in SeqAn3.1.
Member seqan3::HIDDEN: Use seqan3::option_spec::hidden instead.
Member seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent::binning_bitvector::operator!= (binning_bitvector const &lhs, sdsl::bit_vector const &rhs) noexcept: Use binning_bitvector.raw_data() != rhs
Member seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent::binning_bitvector::operator!= (sdsl::bit_vector const &lhs, binning_bitvector const &rhs) noexcept: Use lhs != binning_bitvector.raw_data()
Member seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent::binning_bitvector::operator== (binning_bitvector const &lhs, sdsl::bit_vector const &rhs) noexcept: Use binning_bitvector.raw_data() == rhs
Member seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent::binning_bitvector::operator== (sdsl::bit_vector const &lhs, binning_bitvector const &rhs) noexcept: Use lhs == binning_bitvector.raw_data()
Member seqan3::is_in_alphabet: Use seqan3::char_is_valid_for instead.
Member seqan3::literals::operator "_cigar_op" (char const c) noexcept: Please use seqan3::""_cigar_operation instead.
Member seqan3::literals::operator "_phred68legacy" (char const *s, size_t n): Please use seqan3::operator""_phred68solexa instead.
Member seqan3::literals::operator "_phred68legacy" (char const c) noexcept: Please use seqan3::operator""_phred68solexa instead.
Member seqan3::literals::operator "_sam_dna16" (char const *s, size_t n): Please use seqan3::operator""_dna16sam instead.
Member seqan3::literals::operator "_sam_dna16" (char const c) noexcept: Please use seqan3::operator""_dna16sam instead.
Member seqan3::output_file_validator< file_t >::output_file_validator (std::vector< std::string > extensions): use seqan3::output_file_validator::output_file_validator(mode, extensions)
Class seqan3::overflow_error_on_conversion: Use seqan3::user_input_error instead.
Class seqan3::parser_design_error: Use seqan3::design_error instead.
Class seqan3::parser_invalid_argument: Use seqan3::argument_parser_error instead.
Member seqan3::phred42::phred42 (phred_type const p): This will be removed in 3.1.0. Please use seqan3::phred42::assign_phred() or '!'_phred42.
Member seqan3::phred63::phred63 (phred_type const p): This will be removed in 3.1.0. Please use seqan3::phred63::assign_phred() or '!'_phred63.
Member seqan3::phred68legacy: Please use seqan3::phred68solexa instead.
Member seqan3::phred68solexa::phred68solexa (phred_type const p): This will be removed in 3.1.0. Please use seqan3::phred68solexa::assign_phred() or '!'_phred68solexa.
Member seqan3::phred94::phred94 (phred_type const p): This will be removed in 3.1.0. Please use seqan3::phred94::assign_phred() or '!'_phred94.
Member seqan3::quality_base: Please use seqan3::phred_base instead.
Class seqan3::reference< t >: If t models std::ranges::range use std::ranges::range_reference_t instead or if t models std::input_iterator use std::iter_reference_t instead.
Member seqan3::reference_t: If t models std::ranges::range use std::ranges::range_reference_t instead or if t models std::input_iterator use std::iter_reference_t instead.
Member seqan3::REQUIRED: Use seqan3::option_spec::required instead.
Class seqan3::rvalue_reference< t >: If t models std::ranges::range use std::ranges::range_rvalue_reference_t instead or if t models std::input_iterator use std::iter_rvalue_reference_t instead.
Member seqan3::rvalue_reference_t: If t models std::ranges::range use std::ranges::range_rvalue_reference_t instead or if t models std::input_iterator use std::iter_rvalue_reference_t instead.
Member seqan3::sam_dna16: Please use seqan3::dna16sam instead.
Member seqan3::sam_dna16_vector: Please use seqan3::dna16sam_vector instead.
Member seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::sequence_quality_type: This type will be removed in SeqAn-3.1.0. Use sequence_type and quality_type instead.
Class seqan3::size_type< t >: If t models std::ranges::range use std::ranges::range_size_t instead. If t models std::input_iterator there is no alternative. Unlike std::ranges::range_size_t, the Standard has no std::iter_size_t.
Member seqan3::size_type_t: If t models std::ranges::range use std::ranges::size_type_t instead. If t models std::input_iterator there is no alternative. Unlike std::ranges::range_size_t, the Standard has no std::iter_size_t.
Class seqan3::static_band: use seqan3::align_cfg::band_fixed_size instead.
Member seqan3::translate_triplet (tuple_type const &input_tuple) noexcept: Use seqan3::translate_triplet(nucl_type const & n1, nucl_type const & n2, nucl_type const & n3) instead.
Member seqan3::translate_triplet (range_type &&input_range): Use seqan3::translate_triplet(nucl_type const & n1, nucl_type const & n2, nucl_type const & n3) instead.
Member seqan3::translate_triplet (rng_t &&input_range): Use seqan3::translate_triplet(nucl_type const & n1, nucl_type const & n2, nucl_type const & n3) instead.
Class seqan3::type_conversion_failed: Use seqan3::user_input_error instead.
Class seqan3::validation_failed: Use seqan3::validation_error instead.
Class seqan3::value_type< t >: If t models std::ranges::range use std::ranges::range_value_t instead or if t models std::input_iterator use std::iter_value_t instead.
Member seqan3::value_type_t: If t models std::ranges::range use std::ranges::range_value_t instead or if t models std::input_iterator use std::iter_value_t instead.
Member seqan3::views::drop: Use std::views::drop or seqan3::views::type_reduce | std::views::drop.
Member seqan3::views::to_lower: Use std::views::transform([](auto && chr){return std::tolower(chr)});
Member seqan3::views::to_upper: Use std::views::transform([](auto && chr){return std::toupper(chr)});
File simd_algorithm.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/simd_algorithm.hpp instead.
File simd_algorithm_avx2.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/detail/simd_algorithm_avx2.hpp instead.
File simd_algorithm_avx512.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/detail/simd_algorithm_avx512.hpp instead.
File simd_algorithm_sse4.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/detail/simd_algorithm_sse4.hpp instead.
File single_pass_input.hpp: This header will be removed in 3.1. Please use seqan3/utility/views/single_pass_input.hpp instead.
Member SEQAN3_CPO_IMPL (PRIO, TERM): Please use SEQAN3_CPO_OVERLOAD to define seqan3::detail::customisation_point_object instead.
File simd.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/simd.hpp instead.
File simd_traits.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/simd_traits.hpp instead.
File spin_delay.hpp: This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/utility/parallel/detail/spin_delay.hpp> instead.
File static_band.hpp: This header will be removed in 3.1.0; The contained functionality has been replaced by the seqan3::align_cfg::band_fixed_size configuration.
File template_inspection.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please #include <seqan3/core/detail/template_inspection.hpp> instead.
File to_char.hpp: This header will be removed in 3.1. Please use seqan3/alphabet/views/to_char.hpp instead.
File to_rank.hpp: This header will be removed in 3.1. Please use seqan3/alphabet/views/to_rank.hpp instead.
File to_string.hpp: This header is deprecated and will be removed in SeqAn-3.1.0;. Please #include <seqan3/core/debug_stream/detail/to_string.hpp> instead.
File traits.hpp: This header is deprecated and will be removed in SeqAn-3.1.0;. Please #include <seqan3/utility/type_list/traits.hpp> and <seqan3/utility/type_pack/traits.hpp> instead.
File transform.hpp: This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/utility/char_operations/transform.hpp> instead.
File transformation_trait_or.hpp: This header is deprecated and will be removed in SeqAn-3.1. Please #include <seqan3/utility/type_traits/detail/transformation_trait_or.hpp> instead.
File translate.hpp: This header will be removed in 3.1. Please use seqan3/alphabet/views/translate.hpp instead.
File translate_join.hpp: This header will be removed in 3.1. Please use seqan3/alphabet/views/translate_join.hpp instead.
File trim_quality.hpp: This header will be removed in 3.1. Please use seqan3/alphabet/views/trim_quality.hpp instead.
File tuple.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/tuple/concept.hpp instead.
File tuple_utility.hpp: This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/utility/tuple_utility.hpp> instead.
File type_inspection.hpp: This header is deprecated and will be removed in SeqAn-3.1.0;. Please #include <seqan3/utility/detail/type_name_as_string.hpp> instead.
File type_list.hpp: This header will be removed in 3.1. Please use seqan3/utility/type_list/type_list.hpp instead.
File view_iota_simd.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/views/iota_simd.hpp instead.
File view_to_simd.hpp: This header will be removed in SeqAn-3.1.0. Please use seqan3/utility/simd/views/to_simd.hpp instead.
File zip.hpp: This header will be removed in 3.1. Please use seqan3/utility/views/zip.hpp instead.