Example: Use succinct vectors for histogram construction. More...
#include <iostream>#include <memory>#include <vector>#include <random>#include <algorithm>#include <stdexcept>#include "bm.h"#include "bmtimer.h"#include "bmsparsevec.h"#include "bmsparsevec_compr.h"#include "bmdbg.h"#include "bmundef.h"
Go to the source code of this file.
Typedefs | |
| typedef bm::bvector | bvector_type |
| typedef bvector_type::size_type | bv_size_type |
| typedef bm::sparse_vector< unsigned, bvector_type > | sparse_vector_u32 |
| typedef bm::rsc_sparse_vector< unsigned, sparse_vector_u32 > | rsc_sparse_vector_u32 |
| typedef std::vector< std::pair< bv_size_type, bv_size_type > > | bv_ranges_vector |
Functions | |
| static void | generate_test_data (rsc_sparse_vector_u32 &csv, unsigned size) |
| Generate a test RSC vector with a randomly distributed values imitating distribution density of genome variations it adds a huge area of empty in the middle to simulate chr centromere. More... | |
| static void | generate_access_samples (std::vector< bvector_type::size_type > &sample_vec, unsigned size) |
| generate list of random indexes (locations) to read histogram values More... | |
| static void | compute_historgam (sparse_vector_u32 &hist_sv, const rsc_sparse_vector_u32 &csv, sparse_vector_u32::size_type sampling_size) |
| Compute histogram as a SV vector using fixed sampling interval. More... | |
| static void | compute_rsc_historgam (rsc_sparse_vector_u32 &hist_rsc, const rsc_sparse_vector_u32 &csv, sparse_vector_u32::size_type sampling_size) |
| Compute histogram as a RSC vector using fixed sampling interval. More... | |
| static void | compute_adaptive_rsc_histogram (rsc_sparse_vector_u32 &hist_rsc, const rsc_sparse_vector_u32 &csv, sparse_vector_u32::size_type sampling_size) |
| Adaptive histogram identifies number of not NULL elements (events) and varies the size of the histogram bin trying to make sure all bins (but last) are the same weight. More... | |
| static void | verify_histograms (const rsc_sparse_vector_u32 &hist_rsc, const sparse_vector_u32 &hist_sv, sparse_vector_u32::size_type sampling_size) |
| Some test to confirm correctness. More... | |
| static unsigned long long | access_bench1 (const sparse_vector_u32 &hist_sv, const std::vector< bvector_type::size_type > &sample_vec, unsigned sampling_size) |
| Access benchmark 1. More... | |
| static unsigned long long | access_bench2 (const rsc_sparse_vector_u32 &hist_rsc, const std::vector< bvector_type::size_type > &sample_vec) |
| Access benchmark 2. More... | |
| static void | access_bench3 (const rsc_sparse_vector_u32 &hist_rsc, const std::vector< bvector_type::size_type > &sample_vec, const rsc_sparse_vector_u32 &rsc_data) |
| More... | |
| int | main (void) |
| More... | |
Variables | |
| const unsigned | test_size = 250000000 |
| More... | |
| const unsigned | sampling_interval = 2500 |
| More... | |
| bm::chrono_taker ::duration_map_type | timing_map |
| More... | |
Detailed Description
Example: Use succinct vectors for histogram construction.
Definition in file xsample09.cpp.
Function Documentation
◆ access_bench1()
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static |
Access benchmark 1.
uses regular bit-transposed sparse vector to read histogram values in random order. It relies on fixed inetrval sampling.
- Examples
- xsample09.cpp.
Definition at line 273 of file xsample09.cpp.
Referenced by main().
◆ access_bench2()
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static |
Access benchmark 2.
Uses Rank-Select bit-transposed vector to read histogram values Sampling interval can be non-fixed (variadic, adaptive sampling). Method finds the interval start and value using RSC container not NULL vector
- Examples
- xsample09.cpp.
Definition at line 294 of file xsample09.cpp.
References bm::bvector< Alloc >::find_reverse(), and bm::rsc_sparse_vector< Val, SV >::get_null_bvector().
Referenced by main().
◆ access_bench3()
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static |
- Examples
- xsample09.cpp.
Definition at line 319 of file xsample09.cpp.
References bm::bvector< Alloc >::find(), bm::bvector< Alloc >::find_reverse(), and bm::rsc_sparse_vector< Val, SV >::get_null_bvector().
Referenced by main().
◆ compute_adaptive_rsc_histogram()
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static |
Adaptive histogram identifies number of not NULL elements (events) and varies the size of the histogram bin trying to make sure all bins (but last) are the same weight.
- Examples
- xsample09.cpp.
Definition at line 220 of file xsample09.cpp.
References BM_DECLARE_TEMP_BLOCK, bm::rsc_sparse_vector< Val, SV >::get_null_bvector(), bm::rsc_sparse_vector< Val, SV >::optimize(), bm::rsc_sparse_vector< Val, SV >::push_back(), bm::rank_range_split(), and bm::rsc_sparse_vector< Val, SV >::sync().
Referenced by main().
◆ compute_historgam()
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static |
Compute histogram as a SV vector using fixed sampling interval.
- Examples
- xsample09.cpp.
Definition at line 143 of file xsample09.cpp.
References BM_DECLARE_TEMP_BLOCK, bm::sparse_vector< Val, BV >::get_back_inserter(), bm::rsc_sparse_vector< Val, SV >::get_null_bvector(), bm::sparse_vector< Val, BV >::optimize(), and bm::rsc_sparse_vector< Val, SV >::size().
Referenced by main().
◆ compute_rsc_historgam()
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static |
Compute histogram as a RSC vector using fixed sampling interval.
Histogram values are stored as "true" interval start coordinates and it is a more flexible scheme if we eventually decide to use adaptive sampling (variable step).
- Examples
- xsample09.cpp.
Definition at line 180 of file xsample09.cpp.
References BM_DECLARE_TEMP_BLOCK, bm::rsc_sparse_vector< Val, SV >::get_null_bvector(), bm::rsc_sparse_vector< Val, SV >::load_from(), bm::rsc_sparse_vector< Val, SV >::optimize(), bm::sparse_vector< Val, BV >::set(), bm::rsc_sparse_vector< Val, SV >::size(), bm::rsc_sparse_vector< Val, SV >::sync(), and bm::use_null.
Referenced by main().
◆ generate_access_samples()
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static |
generate list of random indexes (locations) to read histogram values
- Examples
- xsample09.cpp.
Definition at line 124 of file xsample09.cpp.
Referenced by main().
◆ generate_test_data()
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static |
Generate a test RSC vector with a randomly distributed values imitating distribution density of genome variations it adds a huge area of empty in the middle to simulate chr centromere.
- Examples
- xsample09.cpp.
Definition at line 83 of file xsample09.cpp.
References BM_DECLARE_TEMP_BLOCK, bm::rsc_sparse_vector< Val, SV >::get_back_inserter(), bm::rsc_sparse_vector< Val, SV >::optimize(), and bm::rsc_sparse_vector< Val, SV >::sync().
Referenced by main().
◆ main()
| int main | ( | void | ) |
- Examples
- xsample09.cpp.
Definition at line 357 of file xsample09.cpp.
References access_bench1(), access_bench2(), access_bench3(), bm::sparse_vector< Val, BV >::begin(), bm::rsc_sparse_vector< Val, SV >::calc_stat(), bm::sparse_vector< Val, BV >::calc_stat(), compute_adaptive_rsc_histogram(), compute_historgam(), compute_rsc_historgam(), bm::bvector< Alloc >::count(), bm::sparse_vector< Val, BV >::end(), generate_access_samples(), generate_test_data(), bm::rsc_sparse_vector< Val, SV >::get_null_bvector(), bm::chrono_taker< TOut >::print_duration_map(), sampling_interval, bm::sparse_vector< Val, BV >::size(), bm::rsc_sparse_vector< Val, SV >::size(), test_size, timing_map, and verify_histograms().
◆ verify_histograms()
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static |
Some test to confirm correctness.
- Examples
- xsample09.cpp.
Definition at line 246 of file xsample09.cpp.
References bm::rsc_sparse_vector< Val, SV >::get_null_bvector().
Referenced by main().
