BitMagic-C++
Typedefs | Functions | Variables
xsample03.cpp File Reference

Example: SNP search in human genome. More...

#include <iostream>
#include <sstream>
#include <chrono>
#include <regex>
#include <time.h>
#include <stdio.h>
#include <vector>
#include <map>
#include <utility>
#include "bm.h"
#include "bmalgo.h"
#include "bmserial.h"
#include "bmrandom.h"
#include "bmsparsevec.h"
#include "bmsparsevec_compr.h"
#include "bmsparsevec_algo.h"
#include "bmsparsevec_serial.h"
#include "bmalgo_similarity.h"
#include "bmsparsevec_util.h"
#include "bmdbg.h"
#include "bmtimer.h"
#include "bmundef.h"
Include dependency graph for xsample03.cpp:

Go to the source code of this file.

Typedefs

typedef bm::sparse_vector< unsigned, bm::bvector<> > sparse_vector_u32
 
typedef bm::rsc_sparse_vector< unsigned, sparse_vector_u32 > rsc_sparse_vector_u32
 
typedef std::vector< std::pair< unsigned, unsigned > > vector_pairs
 

Functions

static void show_help ()
 
static int parse_args (int argc, char *argv[])
 
static int load_snp_report (const std::string &fname, sparse_vector_u32 &sv)
 
static void generate_random_subset (const sparse_vector_u32 &sv, std::vector< unsigned > &vect, unsigned count)
 
static void build_vector_pairs (const sparse_vector_u32 &sv, vector_pairs &vp)
 
static bool search_vector_pairs (const vector_pairs &vp, unsigned rs_id, unsigned &pos)
 
static void run_benchmark (const sparse_vector_u32 &sv, const rsc_sparse_vector_u32 &csv)
 
int main (int argc, char *argv[])
 

Variables

std::string sv_out_name
 
std::string rsc_out_name
 
std::string sv_in_name
 
std::string rsc_in_name
 
std::string isnp_name
 
bool is_diag = false
 
bool is_timing = false
 
bool is_bench = false
 
bm::chrono_taker::duration_map_type timing_map
 

Detailed Description

Example: SNP search in human genome.

Brief description of used method:

  1. Parse SNP chromosome report and extract information about SNP number and location in the chromosome
  2. Use this information to build bit-transposed sparse_vector<> where vector position matches chromosome position and SNP ids (aka rsid) is kept as a bit-transposed matrix
  3. Build rank-select compressed sparse vector, dropping all NULL columns (this data format is pretty sparse, since number of SNPs is significantly less than number of chromosome bases (1:5 or less) Use memory report to understand memory footprint for each form of storage
  4. Run benchmarks searching for 500 randomly selected SNPs using
    • bm::sparse_vector<>
    • bm::rsc_sparse_vector<>
    • std::vector<pair<unsigned, unsigned> >

This example should be useful for construction of compressed columnar tables with parallel search capabilities.

Definition in file xsample03.cpp.

Typedef Documentation

◆ rsc_sparse_vector_u32

typedef bm::rsc_sparse_vector<unsigned, sparse_vector_u32 > rsc_sparse_vector_u32
Examples:
xsample03.cpp.

Definition at line 205 of file xsample03.cpp.

◆ sparse_vector_u32

typedef bm::sparse_vector<unsigned, bm::bvector<> > sparse_vector_u32
Examples:
xsample03.cpp.

Definition at line 204 of file xsample03.cpp.

◆ vector_pairs

typedef std::vector<std::pair<unsigned, unsigned> > vector_pairs
Examples:
xsample03.cpp.

Definition at line 206 of file xsample03.cpp.

Function Documentation

◆ build_vector_pairs()

static void build_vector_pairs ( const sparse_vector_u32 &  sv,
vector_pairs &  vp 
)
static
Examples:
xsample03.cpp.

Definition at line 312 of file xsample03.cpp.

References bm::sparse_vector< Val, BV >::begin(), bm::sparse_vector< unsigned, bm::bvector<> >::const_iterator, and bm::sparse_vector< Val, BV >::end().

Referenced by run_benchmark().

◆ generate_random_subset()

static void generate_random_subset ( const sparse_vector_u32 &  sv,
std::vector< unsigned > &  vect,
unsigned  count 
)
static
Examples:
xsample03.cpp.

Definition at line 292 of file xsample03.cpp.

References bm::bvector< Alloc >::first(), bm::base_sparse_vector< Val, BV, MAX_SIZE >::get_null_bvector(), bm::sparse_vector< Val, BV >::push_back(), bm::random_subset< BV >::sample(), and bm::bvector< Alloc >::iterator_base::valid().

Referenced by run_benchmark().

◆ load_snp_report()

static int load_snp_report ( const std::string &  fname,
sparse_vector_u32 &  sv 
)
static
Examples:
xsample03.cpp.

Definition at line 218 of file xsample03.cpp.

References bm::bvector< Alloc >::init(), bm::sparse_vector< Val, BV >::set(), bm::bvector< Alloc >::set_bit_no_check(), bm::bvector< Alloc >::test(), and timing_map.

Referenced by main().

◆ main()

int main ( int  argc,
char *  argv[] 
)
Examples:
xsample03.cpp.

Definition at line 460 of file xsample03.cpp.

References bm::chrono_taker::ct_ops_per_sec, bm::rsc_sparse_vector< Val, SV >::empty(), bm::sparse_vector< Val, BV >::empty(), bm::sparse_vector< Val, BV >::equal(), is_bench, is_diag, is_timing, isnp_name, bm::rsc_sparse_vector< Val, SV >::load_from(), load_snp_report(), bm::rsc_sparse_vector< Val, SV >::load_to(), bm::rsc_sparse_vector< Val, SV >::optimize(), bm::sparse_vector< Val, BV >::optimize(), parse_args(), bm::chrono_taker::print_duration_map(), rsc_in_name, rsc_out_name, run_benchmark(), show_help(), sv_in_name, sv_out_name, timing_map, and bm::use_null.

◆ parse_args()

static int parse_args ( int  argc,
char *  argv[] 
)
static
Examples:
xsample03.cpp, xsample07.cpp, and xsample07a.cpp.

Definition at line 110 of file xsample03.cpp.

References is_bench, is_diag, is_timing, isnp_name, rsc_in_name, rsc_out_name, show_help(), sv_in_name, and sv_out_name.

Referenced by main().

◆ run_benchmark()

static void run_benchmark ( const sparse_vector_u32 &  sv,
const rsc_sparse_vector_u32 &  csv 
)
static
Examples:
xsample03.cpp.

Definition at line 349 of file xsample03.cpp.

References build_vector_pairs(), bm::bvector< Alloc >::compare(), bm::rsc_sparse_vector< Val, SV >::empty(), bm::sparse_vector< Val, BV >::empty(), bm::sparse_vector_scanner< SV >::find_eq(), generate_random_subset(), bm::bvector< Alloc >::init(), search_vector_pairs(), bm::bvector< Alloc >::set_bit_no_check(), and timing_map.

Referenced by main().

◆ search_vector_pairs()

static bool search_vector_pairs ( const vector_pairs &  vp,
unsigned  rs_id,
unsigned &  pos 
)
static
Examples:
xsample03.cpp.

Definition at line 330 of file xsample03.cpp.

Referenced by run_benchmark().

◆ show_help()

static void show_help ( )
static
Examples:
xsample03.cpp.

Definition at line 81 of file xsample03.cpp.

Referenced by main(), and parse_args().

Variable Documentation

◆ is_bench

bool is_bench = false
Examples:
xsample03.cpp.

Definition at line 107 of file xsample03.cpp.

Referenced by main(), and parse_args().

◆ is_diag

bool is_diag = false
Examples:
xsample03.cpp.

Definition at line 105 of file xsample03.cpp.

Referenced by main(), and parse_args().

◆ is_timing

bool is_timing = false
Examples:
xsample03.cpp.

Definition at line 106 of file xsample03.cpp.

Referenced by main(), and parse_args().

◆ isnp_name

std::string isnp_name
Examples:
xsample03.cpp.

Definition at line 104 of file xsample03.cpp.

Referenced by main(), and parse_args().

◆ rsc_in_name

std::string rsc_in_name
Examples:
xsample03.cpp.

Definition at line 103 of file xsample03.cpp.

Referenced by main(), and parse_args().

◆ rsc_out_name

std::string rsc_out_name
Examples:
xsample03.cpp.

Definition at line 101 of file xsample03.cpp.

Referenced by main(), and parse_args().

◆ sv_in_name

std::string sv_in_name
Examples:
xsample03.cpp.

Definition at line 102 of file xsample03.cpp.

Referenced by main(), and parse_args().

◆ sv_out_name

std::string sv_out_name
Examples:
xsample03.cpp.

Definition at line 100 of file xsample03.cpp.

Referenced by main(), and parse_args().

◆ timing_map

bm::chrono_taker::duration_map_type timing_map
Examples:
xsample03.cpp.

Definition at line 210 of file xsample03.cpp.

Referenced by load_snp_report(), main(), and run_benchmark().

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