fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
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Namespaces | |
detail | |
hibf | |
Must be first include. | |
index_structure | |
logspace | |
threshold | |
Classes | |
struct | build_arguments |
struct | pattern_size |
struct | search_arguments |
struct | upgrade_arguments |
struct | power_of_two_validator |
class | positive_integer_validator |
class | size_validator |
class | bin_validator |
class | index_factory |
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 | raptor_index |
class | sync_out |
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) |
void raptor::build_from_files | ( | build_arguments const & | arguments | ) |
void raptor::build_from_minimiser | ( | build_arguments const & | arguments | ) |
void raptor::build_parsing | ( | sharg::parser & | parser, |
bool const | is_socks | ||
) |
void raptor::call_parallel_on_bins | ( | algorithm_t && | worker, |
build_arguments const & | arguments | ||
) |
bool raptor::check_for_fasta_format | ( | std::vector< std::string > const & | valid_extensions, |
std::string const & | file_path | ||
) |
void raptor::compute_minimiser | ( | build_arguments const & | arguments | ) |
void raptor::do_parallel | ( | algorithm_t && | worker, |
size_t const | num_records, | ||
size_t const | threads, | ||
double & | compute_time | ||
) |
void raptor::init_build_parser | ( | sharg::parser & | parser, |
build_arguments & | arguments | ||
) |
void raptor::init_search_parser | ( | sharg::parser & | parser, |
search_arguments & | arguments | ||
) |
void raptor::init_shared_meta | ( | sharg::parser & | parser | ) |
void raptor::init_top_level_parser | ( | sharg::parser & | parser | ) |
void raptor::init_upgrade_parser | ( | sharg::parser & | parser, |
upgrade_arguments & | arguments | ||
) |
void raptor::load_index | ( | index_t & | index, |
search_arguments const & | arguments, | ||
double & | index_io_time | ||
) |
void raptor::load_index | ( | index_t & | index, |
search_arguments const & | arguments, | ||
size_t const | part, | ||
double & | index_io_time | ||
) |
void raptor::load_index | ( | index_t & | index, |
std::filesystem::path const & | path, | ||
double & | index_io_time | ||
) |
std::ostream& raptor::operator<< | ( | std::ostream & | s, |
pattern_size const & | |||
) |
std::ostream& raptor::operator<< | ( | std::ostream & | s, |
window const & | |||
) |
std::istream& raptor::operator>> | ( | std::istream & | s, |
pattern_size & | pattern_size_ | ||
) |
std::istream& raptor::operator>> | ( | std::istream & | s, |
window & | window_ | ||
) |
void raptor::parse_bin_path | ( | build_arguments & | arguments | ) |
void raptor::parse_bin_path | ( | upgrade_arguments & | arguments | ) |
void raptor::raptor_build | ( | build_arguments const & | arguments | ) |
void raptor::raptor_search | ( | search_arguments const & | arguments | ) |
void raptor::raptor_upgrade | ( | upgrade_arguments const & | arguments | ) |
void raptor::run_build | ( | sharg::parser & | parser | ) |
void raptor::run_search | ( | sharg::parser & | parser | ) |
void raptor::search_hibf | ( | search_arguments const & | arguments | ) |
template void raptor::search_hibf< false > | ( | search_arguments const & | arguments | ) |
template void raptor::search_hibf< true > | ( | search_arguments const & | arguments | ) |
void raptor::search_ibf | ( | search_arguments const & | arguments | ) |
template void raptor::search_ibf< false > | ( | search_arguments const & | arguments | ) |
template void raptor::search_ibf< true > | ( | search_arguments const & | arguments | ) |
void raptor::search_multiple | ( | search_arguments const & | arguments | ) |
template void raptor::search_multiple< false > | ( | search_arguments const & | arguments | ) |
template void raptor::search_multiple< true > | ( | search_arguments const & | arguments | ) |
void raptor::search_parsing | ( | sharg::parser & | parser, |
bool const | is_socks | ||
) |
void raptor::search_single | ( | search_arguments const & | arguments, |
index_t && | index | ||
) |
void raptor::search_socks | ( | search_arguments const & | arguments | ) |
template void raptor::search_socks< false > | ( | search_arguments const & | arguments | ) |
template void raptor::search_socks< true > | ( | search_arguments const & | arguments | ) |
void raptor::upgrade_index | ( | upgrade_arguments const & | arguments | ) |
void raptor::upgrade_parsing | ( | sharg::parser & | parser | ) |