fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
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Must be first include. More...
Classes | |
struct | build_data |
struct | chopper_pack_record |
struct | node_data |
Functions | |
size_t | bin_size_in_bits (build_arguments const &arguments, size_t const number_of_kmers_to_be_stored) |
template<seqan3::data_layout data_layout_mode> | |
void | chopper_build (build_arguments const &arguments) |
void | compute_kmers (robin_hood::unordered_flat_set< size_t > &kmers, build_arguments const &arguments, chopper_pack_record const &record) |
template<seqan3::data_layout data_layout_mode> | |
seqan3::interleaved_bloom_filter | construct_ibf (robin_hood::unordered_flat_set< size_t > &parent_kmers, robin_hood::unordered_flat_set< size_t > &kmers, size_t const number_of_bins, lemon::ListDigraph::Node const &node, build_data< data_layout_mode > &data, build_arguments const &arguments, bool is_root) |
template<seqan3::data_layout data_layout_mode> | |
void | create_ibfs_from_chopper_pack (build_data< data_layout_mode > &data, build_arguments const &arguments) |
template<seqan3::data_layout data_layout_mode> | |
size_t | hierarchical_build (robin_hood::unordered_flat_set< size_t > &parent_kmers, lemon::ListDigraph::Node const ¤t_node, build_data< data_layout_mode > &data, build_arguments const &arguments, bool is_root) |
template<seqan3::data_layout data_layout_mode> | |
size_t | initialise_max_bin_kmers (robin_hood::unordered_flat_set< size_t > &kmers, std::vector< int64_t > &ibf_positions, std::vector< int64_t > &filename_indices, lemon::ListDigraph::Node const &node, build_data< data_layout_mode > &data, build_arguments const &arguments) |
void | insert_into_ibf (robin_hood::unordered_flat_set< size_t > &parent_kmers, robin_hood::unordered_flat_set< size_t > const &kmers, size_t const number_of_bins, size_t const bin_index, seqan3::interleaved_bloom_filter<> &ibf, bool is_root) |
void | insert_into_ibf (build_arguments const &arguments, chopper_pack_record const &record, seqan3::interleaved_bloom_filter<> &ibf) |
template<seqan3::data_layout data_layout_mode> | |
void | loop_over_children (robin_hood::unordered_flat_set< size_t > &parent_kmers, seqan3::interleaved_bloom_filter<> &ibf, std::vector< int64_t > &ibf_positions, lemon::ListDigraph::Node const ¤t_node, build_data< data_layout_mode > &data, build_arguments const &arguments, bool is_root) |
size_t | parse_chopper_pack_header (lemon::ListDigraph &ibf_graph, lemon::ListDigraph::NodeMap< node_data > &node_map, std::istream &chopper_pack_file) |
chopper_pack_record | parse_chopper_pack_line (std::string const ¤t_line) |
template<seqan3::data_layout data_layout_mode> | |
void | read_chopper_pack_file (build_data< data_layout_mode > &data, std::string const &chopper_pack_filename) |
template<seqan3::data_layout data_layout_mode> | |
void | update_user_bins (build_data< data_layout_mode > &data, std::vector< int64_t > &filename_indices, chopper_pack_record const &record) |
template void | chopper_build< seqan3::data_layout::uncompressed > (build_arguments const &) |
template void | chopper_build< seqan3::data_layout::compressed > (build_arguments const &) |
template seqan3::interleaved_bloom_filter | construct_ibf< seqan3::data_layout::uncompressed > (robin_hood::unordered_flat_set< size_t > &, robin_hood::unordered_flat_set< size_t > &, size_t const, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::uncompressed > &, build_arguments const &, bool) |
template seqan3::interleaved_bloom_filter | construct_ibf< seqan3::data_layout::compressed > (robin_hood::unordered_flat_set< size_t > &, robin_hood::unordered_flat_set< size_t > &, size_t const, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::compressed > &, build_arguments const &, bool) |
template void | create_ibfs_from_chopper_pack< seqan3::data_layout::uncompressed > (build_data< seqan3::data_layout::uncompressed > &, build_arguments const &) |
template void | create_ibfs_from_chopper_pack< seqan3::data_layout::compressed > (build_data< seqan3::data_layout::compressed > &, build_arguments const &arguments) |
template size_t | hierarchical_build< seqan3::data_layout::uncompressed > (robin_hood::unordered_flat_set< size_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::uncompressed > &, build_arguments const &, bool) |
template size_t | hierarchical_build< seqan3::data_layout::compressed > (robin_hood::unordered_flat_set< size_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::compressed > &, build_arguments const &, bool) |
template size_t | initialise_max_bin_kmers< seqan3::data_layout::uncompressed > (robin_hood::unordered_flat_set< size_t > &, std::vector< int64_t > &, std::vector< int64_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::uncompressed > &, build_arguments const &) |
template size_t | initialise_max_bin_kmers< seqan3::data_layout::compressed > (robin_hood::unordered_flat_set< size_t > &, std::vector< int64_t > &, std::vector< int64_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::compressed > &, build_arguments const &) |
template void | loop_over_children< seqan3::data_layout::uncompressed > (robin_hood::unordered_flat_set< size_t > &, seqan3::interleaved_bloom_filter<> &, std::vector< int64_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::uncompressed > &, build_arguments const &, bool) |
template void | loop_over_children< seqan3::data_layout::compressed > (robin_hood::unordered_flat_set< size_t > &, seqan3::interleaved_bloom_filter<> &, std::vector< int64_t > &, lemon::ListDigraph::Node const &, build_data< seqan3::data_layout::compressed > &, build_arguments const &, bool) |
template void | read_chopper_pack_file< seqan3::data_layout::uncompressed > (build_data< seqan3::data_layout::uncompressed > &, std::string const &) |
template void | read_chopper_pack_file< seqan3::data_layout::compressed > (build_data< seqan3::data_layout::compressed > &, std::string const &) |
template void | update_user_bins< seqan3::data_layout::uncompressed > (build_data< seqan3::data_layout::uncompressed > &, std::vector< int64_t > &, chopper_pack_record const &) |
template void | update_user_bins< seqan3::data_layout::compressed > (build_data< seqan3::data_layout::compressed > &, std::vector< int64_t > &, chopper_pack_record const &) |
Variables | |
constexpr std::string_view | hibf_prefix {"HIGH_LEVEL_IBF"} |
constexpr std::string_view | merged_bin_prefix {"MERGED_BIN"} |
constexpr std::string_view | split_bin_prefix {"SPLIT_BIN"} |
constexpr size_t | merged_bin_prefix_length {merged_bin_prefix.size()} |
Must be first include.
size_t raptor::hibf::bin_size_in_bits | ( | build_arguments const & | arguments, |
size_t const | number_of_kmers_to_be_stored | ||
) |
void raptor::hibf::chopper_build | ( | build_arguments const & | arguments | ) |
template void raptor::hibf::chopper_build< seqan3::data_layout::compressed > | ( | build_arguments const & | ) |
template void raptor::hibf::chopper_build< seqan3::data_layout::uncompressed > | ( | build_arguments const & | ) |
void raptor::hibf::compute_kmers | ( | robin_hood::unordered_flat_set< size_t > & | kmers, |
build_arguments const & | arguments, | ||
chopper_pack_record const & | record | ||
) |
seqan3::interleaved_bloom_filter raptor::hibf::construct_ibf | ( | robin_hood::unordered_flat_set< size_t > & | parent_kmers, |
robin_hood::unordered_flat_set< size_t > & | kmers, | ||
size_t const | number_of_bins, | ||
lemon::ListDigraph::Node const & | node, | ||
build_data< data_layout_mode > & | data, | ||
build_arguments const & | arguments, | ||
bool | is_root | ||
) |
template seqan3::interleaved_bloom_filter raptor::hibf::construct_ibf< seqan3::data_layout::compressed > | ( | robin_hood::unordered_flat_set< size_t > & | , |
robin_hood::unordered_flat_set< size_t > & | , | ||
size_t const | , | ||
lemon::ListDigraph::Node const & | , | ||
build_data< seqan3::data_layout::compressed > & | , | ||
build_arguments const & | , | ||
bool | |||
) |
template seqan3::interleaved_bloom_filter raptor::hibf::construct_ibf< seqan3::data_layout::uncompressed > | ( | robin_hood::unordered_flat_set< size_t > & | , |
robin_hood::unordered_flat_set< size_t > & | , | ||
size_t const | , | ||
lemon::ListDigraph::Node const & | , | ||
build_data< seqan3::data_layout::uncompressed > & | , | ||
build_arguments const & | , | ||
bool | |||
) |
void raptor::hibf::create_ibfs_from_chopper_pack | ( | build_data< data_layout_mode > & | data, |
build_arguments const & | arguments | ||
) |
template void raptor::hibf::create_ibfs_from_chopper_pack< seqan3::data_layout::compressed > | ( | build_data< seqan3::data_layout::compressed > & | , |
build_arguments const & | arguments | ||
) |
template void raptor::hibf::create_ibfs_from_chopper_pack< seqan3::data_layout::uncompressed > | ( | build_data< seqan3::data_layout::uncompressed > & | , |
build_arguments const & | |||
) |
size_t raptor::hibf::hierarchical_build | ( | robin_hood::unordered_flat_set< size_t > & | parent_kmers, |
lemon::ListDigraph::Node const & | current_node, | ||
build_data< data_layout_mode > & | data, | ||
build_arguments const & | arguments, | ||
bool | is_root | ||
) |
template size_t raptor::hibf::hierarchical_build< seqan3::data_layout::compressed > | ( | robin_hood::unordered_flat_set< size_t > & | , |
lemon::ListDigraph::Node const & | , | ||
build_data< seqan3::data_layout::compressed > & | , | ||
build_arguments const & | , | ||
bool | |||
) |
template size_t raptor::hibf::hierarchical_build< seqan3::data_layout::uncompressed > | ( | robin_hood::unordered_flat_set< size_t > & | , |
lemon::ListDigraph::Node const & | , | ||
build_data< seqan3::data_layout::uncompressed > & | , | ||
build_arguments const & | , | ||
bool | |||
) |
size_t raptor::hibf::initialise_max_bin_kmers | ( | robin_hood::unordered_flat_set< size_t > & | kmers, |
std::vector< int64_t > & | ibf_positions, | ||
std::vector< int64_t > & | filename_indices, | ||
lemon::ListDigraph::Node const & | node, | ||
build_data< data_layout_mode > & | data, | ||
build_arguments const & | arguments | ||
) |
template size_t raptor::hibf::initialise_max_bin_kmers< seqan3::data_layout::compressed > | ( | robin_hood::unordered_flat_set< size_t > & | , |
std::vector< int64_t > & | , | ||
std::vector< int64_t > & | , | ||
lemon::ListDigraph::Node const & | , | ||
build_data< seqan3::data_layout::compressed > & | , | ||
build_arguments const & | |||
) |
template size_t raptor::hibf::initialise_max_bin_kmers< seqan3::data_layout::uncompressed > | ( | robin_hood::unordered_flat_set< size_t > & | , |
std::vector< int64_t > & | , | ||
std::vector< int64_t > & | , | ||
lemon::ListDigraph::Node const & | , | ||
build_data< seqan3::data_layout::uncompressed > & | , | ||
build_arguments const & | |||
) |
void raptor::hibf::insert_into_ibf | ( | build_arguments const & | arguments, |
chopper_pack_record const & | record, | ||
seqan3::interleaved_bloom_filter<> & | ibf | ||
) |
void raptor::hibf::insert_into_ibf | ( | robin_hood::unordered_flat_set< size_t > & | parent_kmers, |
robin_hood::unordered_flat_set< size_t > const & | kmers, | ||
size_t const | number_of_bins, | ||
size_t const | bin_index, | ||
seqan3::interleaved_bloom_filter<> & | ibf, | ||
bool | is_root | ||
) |
void raptor::hibf::loop_over_children | ( | robin_hood::unordered_flat_set< size_t > & | parent_kmers, |
seqan3::interleaved_bloom_filter<> & | ibf, | ||
std::vector< int64_t > & | ibf_positions, | ||
lemon::ListDigraph::Node const & | current_node, | ||
build_data< data_layout_mode > & | data, | ||
build_arguments const & | arguments, | ||
bool | is_root | ||
) |
template void raptor::hibf::loop_over_children< seqan3::data_layout::compressed > | ( | robin_hood::unordered_flat_set< size_t > & | , |
seqan3::interleaved_bloom_filter<> & | , | ||
std::vector< int64_t > & | , | ||
lemon::ListDigraph::Node const & | , | ||
build_data< seqan3::data_layout::compressed > & | , | ||
build_arguments const & | , | ||
bool | |||
) |
template void raptor::hibf::loop_over_children< seqan3::data_layout::uncompressed > | ( | robin_hood::unordered_flat_set< size_t > & | , |
seqan3::interleaved_bloom_filter<> & | , | ||
std::vector< int64_t > & | , | ||
lemon::ListDigraph::Node const & | , | ||
build_data< seqan3::data_layout::uncompressed > & | , | ||
build_arguments const & | , | ||
bool | |||
) |
size_t raptor::hibf::parse_chopper_pack_header | ( | lemon::ListDigraph & | ibf_graph, |
lemon::ListDigraph::NodeMap< node_data > & | node_map, | ||
std::istream & | chopper_pack_file | ||
) |
chopper_pack_record raptor::hibf::parse_chopper_pack_line | ( | std::string const & | current_line | ) |
void raptor::hibf::read_chopper_pack_file | ( | build_data< data_layout_mode > & | data, |
std::string const & | chopper_pack_filename | ||
) |
template void raptor::hibf::read_chopper_pack_file< seqan3::data_layout::compressed > | ( | build_data< seqan3::data_layout::compressed > & | , |
std::string const & | |||
) |
template void raptor::hibf::read_chopper_pack_file< seqan3::data_layout::uncompressed > | ( | build_data< seqan3::data_layout::uncompressed > & | , |
std::string const & | |||
) |
void raptor::hibf::update_user_bins | ( | build_data< data_layout_mode > & | data, |
std::vector< int64_t > & | filename_indices, | ||
chopper_pack_record const & | record | ||
) |
template void raptor::hibf::update_user_bins< seqan3::data_layout::compressed > | ( | build_data< seqan3::data_layout::compressed > & | , |
std::vector< int64_t > & | , | ||
chopper_pack_record const & | |||
) |
template void raptor::hibf::update_user_bins< seqan3::data_layout::uncompressed > | ( | build_data< seqan3::data_layout::uncompressed > & | , |
std::vector< int64_t > & | , | ||
chopper_pack_record const & | |||
) |
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