18#include <seqan3/search/kmer_index/shape.hpp>
30 uint32_t window_size{20u};
31 seqan3::shape shape{seqan3::ungapped{20u}};
32 uint8_t shape_size{shape.size()};
33 uint8_t shape_weight{shape.count()};
42 uint64_t query_length{};
47 bool compressed{
false};
53 bool write_time{
false};
55 bool cache_thresholds{
false};
67 void print_timings()
const
72 std::cerr <<
"Wall clock time [s]: " << wall_clock_timer.in_seconds() <<
'\n';
73 std::cerr <<
"Peak memory usage " << formatted_peak_ram() <<
'\n';
74 std::cerr <<
"Determine query length [s]: " << query_length_timer.in_seconds() <<
'\n';
75 std::cerr <<
"Query file I/O [s]: " << query_file_io_timer.in_seconds() <<
'\n';
76 std::cerr <<
"Load index [s]: " << load_index_timer.in_seconds() <<
'\n';
77 std::cerr <<
"Compute minimiser [s]: " << compute_minimiser_timer.in_seconds() / threads <<
'\n';
78 std::cerr <<
"Query IBF [s]: " << query_ibf_timer.in_seconds() / threads <<
'\n';
79 std::cerr <<
"Generate results [s]: " << generate_results_timer.in_seconds() / threads <<
'\n';
84 return {.window_size{window_size},
86 .query_length{query_length},
88 .percentage{threshold},
91 .cache_thresholds{cache_thresholds},
Provides raptor::formatted_peak_ram.
T setprecision(T... args)
Definition: search_arguments.hpp:28
Definition: threshold_parameters.hpp:23
Provides raptor::threshold::threshold_parameters.