fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
Namespaces | Classes | Functions
raptor Namespace Reference

Namespaces

namespace  detail
 
namespace  hibf
 Must be first include.
 
namespace  index_structure
 
namespace  logspace
 
namespace  threshold
 

Classes

class  bin_validator
 
struct  build_arguments
 
struct  dna4_traits
 
class  hierarchical_interleaved_bloom_filter
 The HIBF binning directory. A data structure that efficiently answers set-membership queries for multiple bins. More...
 
class  index_factory
 
struct  pattern_size
 
class  positive_integer_validator
 
struct  power_of_two_validator
 
class  raptor_index
 
struct  search_arguments
 
class  size_validator
 
class  sync_out
 
struct  upgrade_arguments
 
struct  window
 Strong type for passing the window size. More...
 

Functions

void build_parsing (sharg::parser &parser, bool const is_socks)
 
void init_shared_meta (sharg::parser &parser)
 
void parse_bin_path (build_arguments &arguments)
 
void parse_bin_path (upgrade_arguments &arguments)
 
void search_parsing (sharg::parser &parser, bool const is_socks)
 
void upgrade_parsing (sharg::parser &parser)
 
template<bool compressed>
void build_from_files (build_arguments const &arguments)
 
void build_from_minimiser (build_arguments const &arguments)
 
template<typename algorithm_t >
void call_parallel_on_bins (algorithm_t &&worker, build_arguments const &arguments)
 
void compute_minimiser (build_arguments const &arguments)
 
void raptor_build (build_arguments const &arguments)
 
void init_top_level_parser (sharg::parser &parser)
 
void run_build (sharg::parser &parser)
 
void run_search (sharg::parser &parser)
 
template<typename algorithm_t >
void do_parallel (algorithm_t &&worker, size_t const num_records, size_t const threads, double &compute_time)
 
template<typename index_t >
void load_index (index_t &index, search_arguments const &arguments, size_t const part, double &index_io_time)
 
template<typename index_t >
void load_index (index_t &index, search_arguments const &arguments, double &index_io_time)
 
template<typename index_t >
void load_index (index_t &index, std::filesystem::path const &path, double &index_io_time)
 
void raptor_search (search_arguments const &arguments)
 
template<bool compressed>
void search_hibf (search_arguments const &arguments)
 
template<bool compressed>
void search_ibf (search_arguments const &arguments)
 
template<bool compressed>
void search_multiple (search_arguments const &arguments)
 
template<typename index_t >
void search_single (search_arguments const &arguments, index_t &&index)
 
template<bool compressed>
void search_socks (search_arguments const &arguments)
 
void raptor_upgrade (upgrade_arguments const &arguments)
 
template<bool compressed>
void upgrade_index (upgrade_arguments const &arguments)
 
std::ostream & operator<< (std::ostream &s, window const &)
 
std::istream & operator>> (std::istream &s, window &window_)
 
void init_build_parser (sharg::parser &parser, build_arguments &arguments)
 
std::ostream & operator<< (std::ostream &s, pattern_size const &)
 
std::istream & operator>> (std::istream &s, pattern_size &pattern_size_)
 
void init_search_parser (sharg::parser &parser, search_arguments &arguments)
 
void init_upgrade_parser (sharg::parser &parser, upgrade_arguments &arguments)
 
bool check_for_fasta_format (std::vector< std::string > const &valid_extensions, std::string const &file_path)
 
template void search_hibf< false > (search_arguments const &arguments)
 
template void search_hibf< true > (search_arguments const &arguments)
 
template void search_ibf< false > (search_arguments const &arguments)
 
template void search_ibf< true > (search_arguments const &arguments)
 
template void search_multiple< false > (search_arguments const &arguments)
 
template void search_multiple< true > (search_arguments const &arguments)
 
template void search_socks< false > (search_arguments const &arguments)
 
template void search_socks< true > (search_arguments const &arguments)
 

Function Documentation

◆ build_from_files()

template<bool compressed>
void raptor::build_from_files ( build_arguments const &  arguments)

◆ build_from_minimiser()

void raptor::build_from_minimiser ( build_arguments const &  arguments)

◆ build_parsing()

void raptor::build_parsing ( sharg::parser &  parser,
bool const  is_socks 
)

◆ call_parallel_on_bins()

template<typename algorithm_t >
void raptor::call_parallel_on_bins ( algorithm_t &&  worker,
build_arguments const &  arguments 
)

◆ check_for_fasta_format()

bool raptor::check_for_fasta_format ( std::vector< std::string > const &  valid_extensions,
std::string const &  file_path 
)

◆ compute_minimiser()

void raptor::compute_minimiser ( build_arguments const &  arguments)

◆ do_parallel()

template<typename algorithm_t >
void raptor::do_parallel ( algorithm_t &&  worker,
size_t const  num_records,
size_t const  threads,
double &  compute_time 
)

◆ init_build_parser()

void raptor::init_build_parser ( sharg::parser &  parser,
build_arguments arguments 
)

◆ init_search_parser()

void raptor::init_search_parser ( sharg::parser &  parser,
search_arguments arguments 
)

◆ init_shared_meta()

void raptor::init_shared_meta ( sharg::parser &  parser)

◆ init_top_level_parser()

void raptor::init_top_level_parser ( sharg::parser &  parser)

◆ init_upgrade_parser()

void raptor::init_upgrade_parser ( sharg::parser &  parser,
upgrade_arguments arguments 
)

◆ load_index() [1/3]

template<typename index_t >
void raptor::load_index ( index_t &  index,
search_arguments const &  arguments,
double &  index_io_time 
)

◆ load_index() [2/3]

template<typename index_t >
void raptor::load_index ( index_t &  index,
search_arguments const &  arguments,
size_t const  part,
double &  index_io_time 
)

◆ load_index() [3/3]

template<typename index_t >
void raptor::load_index ( index_t &  index,
std::filesystem::path const &  path,
double &  index_io_time 
)

◆ operator<<() [1/2]

std::ostream & raptor::operator<< ( std::ostream &  s,
pattern_size const &   
)

◆ operator<<() [2/2]

std::ostream & raptor::operator<< ( std::ostream &  s,
window const &   
)

◆ operator>>() [1/2]

std::istream & raptor::operator>> ( std::istream &  s,
pattern_size pattern_size_ 
)

◆ operator>>() [2/2]

std::istream & raptor::operator>> ( std::istream &  s,
window window_ 
)

◆ parse_bin_path() [1/2]

void raptor::parse_bin_path ( build_arguments arguments)

◆ parse_bin_path() [2/2]

void raptor::parse_bin_path ( upgrade_arguments arguments)

◆ raptor_build()

void raptor::raptor_build ( build_arguments const &  arguments)

◆ raptor_search()

void raptor::raptor_search ( search_arguments const &  arguments)

◆ raptor_upgrade()

void raptor::raptor_upgrade ( upgrade_arguments const &  arguments)

◆ run_build()

void raptor::run_build ( sharg::parser &  parser)

◆ run_search()

void raptor::run_search ( sharg::parser &  parser)

◆ search_hibf()

template<bool compressed>
void raptor::search_hibf ( search_arguments const &  arguments)

◆ search_hibf< false >()

template void raptor::search_hibf< false > ( search_arguments const &  arguments)

◆ search_hibf< true >()

template void raptor::search_hibf< true > ( search_arguments const &  arguments)

◆ search_ibf()

template<bool compressed>
void raptor::search_ibf ( search_arguments const &  arguments)

◆ search_ibf< false >()

template void raptor::search_ibf< false > ( search_arguments const &  arguments)

◆ search_ibf< true >()

template void raptor::search_ibf< true > ( search_arguments const &  arguments)

◆ search_multiple()

template<bool compressed>
void raptor::search_multiple ( search_arguments const &  arguments)

◆ search_multiple< false >()

template void raptor::search_multiple< false > ( search_arguments const &  arguments)

◆ search_multiple< true >()

template void raptor::search_multiple< true > ( search_arguments const &  arguments)

◆ search_parsing()

void raptor::search_parsing ( sharg::parser &  parser,
bool const  is_socks 
)

◆ search_single()

template<typename index_t >
void raptor::search_single ( search_arguments const &  arguments,
index_t &&  index 
)

◆ search_socks()

template<bool compressed>
void raptor::search_socks ( search_arguments const &  arguments)

◆ search_socks< false >()

template void raptor::search_socks< false > ( search_arguments const &  arguments)

◆ search_socks< true >()

template void raptor::search_socks< true > ( search_arguments const &  arguments)

◆ upgrade_index()

template<bool compressed>
void raptor::upgrade_index ( upgrade_arguments const &  arguments)

◆ upgrade_parsing()

void raptor::upgrade_parsing ( sharg::parser &  parser)