SeqAn3
3.4.0-rc.4
The Modern C++ library for sequence analysis.
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Setup
Setting up library tests
Quick Setup (using CMake)
Tutorial
First steps with SeqAn
Parsing command line arguments with Sharg
C++ Concepts
Alphabets in SeqAn
Ranges
Minimisers
Sequence File Input and Output
Pairwise Alignment
Indexing and searching with SeqAn
SAM Input and Output in SeqAn
Implementing your own read mapper with SeqAn
How-To
Porting from SeqAn2
How to write an argument parser with subcommands
How to serialise SeqAn data structures
How to write a view
How to write your own alphabet
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Here is a list of all documented namespace functions with links to the namespaces they belong to:
- a -
align_pairwise() :
seqan3
alignment_from_cigar() :
seqan3
alignment_result_value_type() :
seqan3::detail
all_elements_model_totally_ordered() :
seqan3::detail
all_of() :
seqan3::detail
- b -
bi_fm_index() :
seqan3
bpp_from_rna_structure() :
seqan3::detail
- c -
call_server() :
seqan3::detail
ceil_log2() :
seqan3::detail
cigar_from_alignment() :
seqan3
compute_ss() :
seqan3::detail
consume() :
seqan3::detail
- e -
extract_eighth() :
seqan3::detail
extract_eighth_avx2() :
seqan3::detail
extract_eighth_avx512() :
seqan3::detail
extract_eighth_sse4() :
seqan3::detail
extract_half() :
seqan3::detail
extract_half_avx2() :
seqan3::detail
extract_half_avx512() :
seqan3::detail
extract_half_sse4() :
seqan3::detail
extract_impl() :
seqan3::detail
extract_quarter() :
seqan3::detail
extract_quarter_avx2() :
seqan3::detail
extract_quarter_avx512() :
seqan3::detail
extract_quarter_sse4() :
seqan3::detail
- f -
fill() :
seqan3::simd
fill_impl() :
seqan3::detail
floor_log2() :
seqan3::detail
fm_index() :
seqan3
for_each() :
seqan3::detail
- g -
gap_decorator() :
seqan3
get() :
seqan3
get_cigar_string() :
seqan3::detail
get_or() :
seqan3::detail
get_or_ignore() :
seqan3::detail
get_terminal_width() :
seqan3::detail
- i -
iota() :
seqan3::simd
iota_impl() :
seqan3::detail
is_terminal() :
seqan3::detail
- k -
kmer_hash_view() :
seqan3::detail
- l -
load() :
seqan3::simd
load_avx2() :
seqan3::detail
load_avx512() :
seqan3::detail
load_sse4() :
seqan3::detail
- m -
make_printable() :
seqan3::detail
make_secondary_istream() :
seqan3::detail
make_secondary_ostream() :
seqan3::detail
minimiser_view() :
seqan3::detail
multi_invocable() :
seqan3::detail
- o -
on_result() :
seqan3::align_cfg
,
seqan3::search_cfg
operator""_cigar_operation() :
seqan3::literals
operator""_db3() :
seqan3::literals
operator""_dna15() :
seqan3::literals
operator""_dna16sam() :
seqan3::literals
operator""_dna3bs() :
seqan3::literals
operator""_dna4() :
seqan3::literals
operator""_dna5() :
seqan3::literals
operator""_dssp9() :
seqan3::literals
operator""_phred42() :
seqan3::literals
operator""_phred63() :
seqan3::literals
operator""_phred68solexa() :
seqan3::literals
operator""_phred94() :
seqan3::literals
operator""_rna15() :
seqan3::literals
operator""_rna4() :
seqan3::literals
operator""_rna5() :
seqan3::literals
operator""_shape() :
seqan3::literals
operator""_tag() :
seqan3::literals
operator""_wuss51() :
seqan3::literals
operator|() :
seqan3
- p -
pairwise_combine_view() :
seqan3::detail
parse_cigar() :
seqan3::detail
pow() :
seqan3
print_tuple() :
seqan3::detail
- r -
range_wrap_ignore() :
seqan3::detail
remove_gap_from_value_type() :
seqan3::detail
- s -
search() :
seqan3
search_scheme_block_info() :
seqan3::detail
search_ss() :
seqan3::detail
search_ss_children() :
seqan3::detail
search_ss_deletion() :
seqan3::detail
search_ss_exact() :
seqan3::detail
set_format() :
seqan3::detail
small_vector() :
seqan3
starts_with() :
seqan3::detail
store() :
seqan3::simd
store_avx2() :
seqan3::detail
store_avx512() :
seqan3::detail
store_sse4() :
seqan3::detail
stream_alignment() :
seqan3::detail
- t -
to_little_endian() :
seqan3::detail
to_lower() :
seqan3
to_string() :
seqan3::detail
to_upper() :
seqan3
translate_triplet() :
seqan3
transpose() :
seqan3::simd
transpose_matrix_avx2() :
seqan3::detail
transpose_matrix_avx512() :
seqan3::detail
transpose_matrix_sse4() :
seqan3::detail
tuple_pop_front() :
seqan3
tuple_split() :
seqan3::detail
,
seqan3
- u -
upcast() :
seqan3::simd
upcast_signed() :
seqan3::detail
upcast_signed_avx2() :
seqan3::detail
upcast_signed_avx512() :
seqan3::detail
upcast_signed_sse4() :
seqan3::detail
upcast_unsigned() :
seqan3::detail
upcast_unsigned_avx2() :
seqan3::detail
upcast_unsigned_avx512() :
seqan3::detail
upcast_unsigned_sse4() :
seqan3::detail
update_alignment_lengths() :
seqan3::detail
- v -
valid_file_extensions() :
seqan3::detail
view_translate() :
seqan3::detail
view_translate_join() :
seqan3::detail
view_translate_single() :
seqan3::detail
- w -
write_eol() :
seqan3::detail
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