Alignment

namespace seqan3

The main SeqAn3 namespace.

Helpers for seqan3::semi_alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::semi_alphabet_concept.

Helpers for seqan3::alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::alphabet_concept.

Helpers for seqan3::nucleotide_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::nucleotide_concept.

Alphabet aliases

Other names (typedefs) for seqan3::nucl16

Range concepts

Adapted from the Ranges TS.

Container concepts

Container concepts as defined by the standard library (or very close).

Container-of-container concepts

Shortcuts for multi-dimensional container concepts.

Enums

enum align_record_fields

Values:

RAW_SCORE
BIT_SCORE
EDIT_DISTANCE
PERCENT_IDENTITY

Variables

concept bool seqan3::align_file_traits_concept = requires (t v) { t::stream_type; t::valid_formats; t::valid_compression_formats; t::query_seqs_type; t::query_ids_type; t::subject_seqs_type; t::subject_ids_type; t::qry_gaps_type; t::sbj_gaps_type; }
char align_record_fields_sam_bam_tags[2][] = { "AS", "BS", "NM", ... }
std::string align_record_field_labels[] = { "raw score" "bit score", "edit distance", ... }
namespace detail

The internal SeqAn3 namespace.

The contents of this namespace are not visible to consumers of the library and the documentation is only generated for developers.

See
https://github.com/seqan/seqan3/wiki/Documentation

template <typename align_file_traits>
class align_file

Public Functions

align_file(std::string const &_file_name)
align_file(align_file const&)
align_file &operator=(align_file const&)
align_file(align_file&&)
align_file &operator=(align_file&&)
void set_store(std::tuple<query_seqs_type const&, query_ids_type const&, subject_seqs_type const&, subject_ids_type const&> const&)

Public Members

options_type options

Protected Functions

~align_file()
void select_decompression(std::string const &compress_ext)
template <size_t index>
void assign_format(std::string const &ext)

Protected Attributes

std::string file_name
stream_type stream
valid_formats format
store_type store
struct align_record

Public Types

template<>
using field_variant = std::variant<int8_t, uint8_t, int16_t, uint16_t, int32_t, uint32_t, int64_t, uint64_t, float, double, std::string, std::string_view, ranges::any_random_access_view<char&>, ranges::any_random_access_view<char>, std::vector<int8_t>, std::vector<uint8_t>, std::vector<int16_t>, std::vector<uint16_t>, std::vector<int32_t>, std::vector<uint32_t>, std::vector<int64_t>, std::vector<uint64_t>, std::vector<float>, std::vector<double>>

Public Members

template<>
size_t qry_no
template<>
size_t qry_begin
template<>
size_t qry_end
template<>
size_t sbj_no
template<>
size_t sbj_begin
template<>
size_t sbj_end
template<>
align_file_traits::query_gaps_type qry_gaps
template<>
align_file_traits::subject_gaps_type sbj_gaps
struct options_type

Public Members

template<>
std::string program_name
template<>
std::string program_version
template<>
std::string command_line
template<>
std::vector<std::string> additional_comment_lines
template<>
bool sorted_by_query
namespace seqan3

The main SeqAn3 namespace.

Helpers for seqan3::semi_alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::semi_alphabet_concept.

Helpers for seqan3::alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::alphabet_concept.

Helpers for seqan3::nucleotide_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::nucleotide_concept.

Alphabet aliases

Other names (typedefs) for seqan3::nucl16

Range concepts

Adapted from the Ranges TS.

Container concepts

Container concepts as defined by the standard library (or very close).

Container-of-container concepts

Shortcuts for multi-dimensional container concepts.

Functions

template <typename record_type>
requires seqan3::align_record_concept< record_type >(requires container_concept < record_type > &&requires align_record_concept< typename record_type::value_type >)
template <typename align_file_in_traits = align_file_in_default_dna_traits>
class align_file_in

Inherits from seqan3::detail::align_file< align_file_in_traits >

Public Functions

align_file_in(std::string const &_file_name)
align_file_in(align_file_in const&)
align_file_in &operator=(align_file_in const&)
align_file_in(align_file_in&&)
align_file_in &operator=(align_file_in&&)
template <typename record_type>
requires seqan3::align_file_in::align_record_concept(requires container_concept < record_type > &&requires align_record_concept< typename record_type::value_type >)
template <typename... types>
void read_raw(...)
void set_store(std::tuple<subject_seqs_type const&, subject_ids_type const&> const&)
template <typename... arg_types>
void read_raw(arg_types&&... args)

Protected Functions

~align_file_in()

Protected Attributes

store_type store
struct store_type

Public Members

template<>
align_file_in_traits::query_seqs_type *qry_seqs = {nullptr}
template<>
align_file_in_traits::query_ids_type *qry_ids = {nullptr}
template<>
align_file_in_traits::subject_seqs_type *sbj_seqs = {nullptr}
template<>
align_file_in_traits::subject_ids_type *sbj_ids = {nullptr}
template<>
align_file_in_traits::query_seqs_type qry_seqs_from_file
template<>
align_file_in_traits::query_ids_type qry_ids_from_file
template<>
align_file_in_traits::subject_seqs_type sbj_seqs_from_file
template<>
align_file_in_traits::subject_ids_type sbj_ids_from_file
template<>
align_file_in_traits::query_id_map_type query_id_map
template<>
align_file_in_traits::subject_id_map_type subject_id_map
struct align_file_in_default_aa_traits

Inherits from seqan3::align_file_in_default_dna_traits

Public Types

using query_seqs_type = std::vector<aa27_vector>
using subject_seqs_type = std::vector<aa27_vector>
using stream_type = std::ifstream
using valid_formats = std::variant<align_file_in_format_sam, align_file_in_format_bam, align_file_in_format_blast_tabular align_file_in_format_blast_tabular_comments>
using query_ids_type = std::vector<std::string>
using subject_ids_type = std::vector<std::string>

Public Static Attributes

constexpr std::vector<std::pair<std::string, void>> valid_compression_formats = {}
struct align_file_in_default_dna_traits

Subclassed by seqan3::align_file_in_default_aa_traits

Public Types

using stream_type = std::ifstream
using valid_formats = std::variant<align_file_in_format_sam, align_file_in_format_bam, align_file_in_format_blast_tabular align_file_in_format_blast_tabular_comments>
using query_seqs_type = std::vector<dna_vector>
using query_ids_type = std::vector<std::string>
using subject_seqs_type = std::vector<dna_vector>
using subject_ids_type = std::vector<std::string>

Public Static Attributes

constexpr std::vector<std::pair<std::string, void>> valid_compression_formats = {}
namespace seqan3

The main SeqAn3 namespace.

Helpers for seqan3::semi_alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::semi_alphabet_concept.

Helpers for seqan3::alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::alphabet_concept.

Helpers for seqan3::nucleotide_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::nucleotide_concept.

Alphabet aliases

Other names (typedefs) for seqan3::nucl16

Range concepts

Adapted from the Ranges TS.

Container concepts

Container concepts as defined by the standard library (or very close).

Container-of-container concepts

Shortcuts for multi-dimensional container concepts.

template <typename align_file_out_traits = align_file_out_default_dna_traits>
class align_file_out

Inherits from seqan3::detail::align_file< align_file_out_traits >

Public Functions

align_file_out(std::string const &_file_name)
align_file_out(align_file_out const&)
align_file_out &operator=(align_file_out const&)
align_file_out(align_file_out&&)
align_file_out &operator=(align_file_out&&)
template <typename record_type>
requires seqan3::align_file_out::align_record_concept(requires container_concept < record_type > &&requires align_record_concept< typename record_type::value_type >)
template <typename... types>
void write_raw(...)
template <typename... arg_types>
void write_raw(arg_types&&... args)

Protected Functions

~align_file_out()

Protected Attributes

store_type store
struct store_type

Public Members

template<>
align_file_out_traits::query_seqs_type *qry_seqs = {nullptr}
template<>
align_file_out_traits::query_ids_type *qry_ids = {nullptr}
template<>
align_file_out_traits::subject_seqs_type *sbj_seqs = {nullptr}
template<>
align_file_out_traits::subject_ids_type *sbj_ids = {nullptr}
struct align_file_out_default_aa_traits

Inherits from seqan3::align_file_out_default_dna_traits

Public Types

using query_seqs_type = std::vector<aa27_vector>
using subject_seqs_type = std::vector<aa27_vector>
using stream_type = std::ifstream
using valid_formats = std::variant<align_file_out_format_sam, align_file_out_format_bam, align_file_out_format_blast_tabular align_file_out_format_blast_tabular_comments, align_file_out_format_blast_report>
using query_ids_type = std::vector<std::string>
using subject_ids_type = std::vector<std::string>

Public Static Attributes

constexpr std::vector<std::pair<std::string, void>> valid_compression_formats = {}
struct align_file_out_default_dna_traits

Subclassed by seqan3::align_file_out_default_aa_traits

Public Types

using stream_type = std::ifstream
using valid_formats = std::variant<align_file_out_format_sam, align_file_out_format_bam, align_file_out_format_blast_tabular align_file_out_format_blast_tabular_comments, align_file_out_format_blast_report>
using query_seqs_type = std::vector<dna_vector>
using query_ids_type = std::vector<std::string>
using subject_seqs_type = std::vector<dna_vector>
using subject_ids_type = std::vector<std::string>

Public Static Attributes

constexpr std::vector<std::pair<std::string, void>> valid_compression_formats = {}