18#include <seqan3/search/kmer_index/shape.hpp>
30 uint8_t kmer_size{20u};
31 uint32_t window_size{kmer_size};
33 seqan3::shape shape{seqan3::ungapped{kmer_size}};
38 mutable uint64_t bits{4096};
42 bool compressed{
false};
49 bool input_is_minimiser{
false};
61 void print_timings()
const
66 std::cerr <<
"Wall clock time [s]: " << wall_clock_timer.in_seconds() <<
'\n';
67 std::cerr <<
"Peak memory usage " << formatted_peak_ram() <<
'\n';
69 std::cerr <<
"Determine IBF size [s]: " << bin_size_timer.in_seconds() <<
'\n';
70 std::cerr <<
"Index allocation [s]: " << index_allocation_timer.in_seconds() <<
'\n';
71 std::cerr <<
"User bin I/O avg per thread [s]: " << user_bin_io_timer.in_seconds() / threads <<
'\n';
72 std::cerr <<
"User bin I/O sum [s]: " << user_bin_io_timer.in_seconds() <<
'\n';
75 std::cerr <<
"Merge kmer sets avg per thread [s]: " << merge_kmers_timer.in_seconds() / threads <<
'\n';
76 std::cerr <<
"Merge kmer sets sum [s]: " << merge_kmers_timer.in_seconds() <<
'\n';
78 std::cerr <<
"Fill IBF avg per thread [s]: " << fill_ibf_timer.in_seconds() / threads <<
'\n';
79 std::cerr <<
"Fill IBF sum [s]: " << fill_ibf_timer.in_seconds() <<
'\n';
80 std::cerr <<
"Store index [s]: " << store_index_timer.in_seconds() <<
'\n';
Provides raptor::formatted_peak_ram.
T setprecision(T... args)
Definition: build_arguments.hpp:28