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 () |
| More... | |
| static int | parse_args (int argc, char *argv[]) |
| More... | |
| static int | load_snp_report (const std::string &fname, sparse_vector_u32 &sv) |
| More... | |
| static void | generate_random_subset (const sparse_vector_u32 &sv, std::vector< unsigned > &vect, unsigned count) |
| More... | |
| static void | build_vector_pairs (const sparse_vector_u32 &sv, vector_pairs &vp) |
| More... | |
| static bool | search_vector_pairs (const vector_pairs &vp, unsigned rs_id, unsigned &pos) |
| More... | |
| static void | run_benchmark (const sparse_vector_u32 &sv, const rsc_sparse_vector_u32 &csv) |
| More... | |
| int | main (int argc, char *argv[]) |
| More... | |
Variables | |
| std::string | sv_out_name |
| More... | |
| std::string | rsc_out_name |
| More... | |
| std::string | sv_in_name |
| More... | |
| std::string | rsc_in_name |
| More... | |
| std::string | isnp_name |
| More... | |
| bool | is_diag = false |
| More... | |
| bool | is_timing = false |
| More... | |
| bool | is_bench = false |
| More... | |
| bm::chrono_taker ::duration_map_type | timing_map |
| More... | |
Detailed Description
Example: SNP search in human genome.
Brief description of used method:
- Parse SNP chromosome report and extract information about SNP number and location in the chromosome
- 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
- 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
- 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.
