9#include <seqan3/alphabet/nucleotide/dna4.hpp>
10#include <seqan3/io/sequence_file/input.hpp>
11#include <seqan3/search/dream_index/interleaved_bloom_filter.hpp>
12#include <seqan3/search/kmer_index/shape.hpp>
13#include <seqan3/search/views/minimiser_hash.hpp>
15static inline constexpr uint64_t adjust_seed(uint8_t
const kmer_size,
16 uint64_t
const seed = 0x8F'3F'73'B5'CF'1C'9A'DEULL) noexcept
18 return seed >> (64u - 2u * kmer_size);
32 seqan3::seed
s{0x8F'3F'73'B5'CF'1C'9A'DEULL};
33 seqan3::shape
shape = seqan3::ungapped{
k};
45 template <
class Archive>
46 void save(Archive & archive)
const
58 template <
class Archive>
59 void load(Archive & archive)
78 std::ifstream is{ipath, std::ios::binary};
79 cereal::BinaryInputArchive iarchive{is};
89 std::ofstream os{opath, std::ios::binary};
90 cereal::BinaryOutputArchive oarchive{os};
95struct my_traits : seqan3::sequence_file_input_default_traits_dna
107template <
class IBFType>
110 std::ifstream is{ipath, std::ios::binary};
111 cereal::BinaryInputArchive iarchive{is};
119template <
class IBFType>
122 std::ofstream os{opath, std::ios::binary};
123 cereal::BinaryOutputArchive oarchive{os};
std::vector< uint16_t > ibf(std::vector< std::filesystem::path > const &sequence_files, estimate_ibf_arguments &ibf_args, minimiser_arguments &minimiser_args, std::vector< double > &fpr, std::vector< uint8_t > &cutoffs, std::filesystem::path const expression_by_genome_file="", size_t num_hash=1)
Creates IBFs.
Definition ibf.cpp:1025
void load_ibf(IBFType &ibf, std::filesystem::path ipath)
Function, loading compressed and uncompressed ibfs.
Definition shared.hpp:108
void store_ibf(IBFType const &ibf, std::filesystem::path opath)
Function, which stored compressed and uncompressed ibfs.
Definition shared.hpp:120
arguments used for all tools
Definition shared.hpp:23
uint8_t threads
Definition shared.hpp:25
std::filesystem::path path_out
Definition shared.hpp:24
arguments used for estimate, ibf, ibfmin
Definition shared.hpp:39
void load(Archive &archive)
Definition shared.hpp:59
std::vector< uint16_t > expression_thresholds
Definition shared.hpp:41
uint8_t number_expression_thresholds
Definition shared.hpp:42
bool compressed
Definition shared.hpp:40
bool samplewise
Definition shared.hpp:43
void save(Archive &archive) const
Definition shared.hpp:46
arguments used for estimate, ibf, minimiser
Definition shared.hpp:30
uint8_t k
Definition shared.hpp:31
seqan3::shape shape
Definition shared.hpp:33
seqan3::window_size w_size
Definition shared.hpp:34
seqan3::seed s
Definition shared.hpp:32
Use dna4 instead of default dna5.
Definition shared.hpp:96
seqan3::dna4 sequence_alphabet
Definition shared.hpp:97