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bootstrap.h
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bootstrap.h
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/**
* @file bootstrap.h
* @brief header file for bootstrap.cpp
* @details contains block bootstrapping related data structures and functions
*/
#ifndef __BOOTSTRAP_H__
#define __BOOTSTRAP_H__
/* INCLUDES ----------------------------------------------------------------- */
#include "dataStructs.h"
#include "shared.h"
/* END-OF-INCLUDES ---------------------------------------------------------- */
/* FORWARD-DECLARATIONS ----------------------------------------------------- */
typedef struct bblocks_t bblocks_t;
typedef struct strArray strArray;
void strArray_destroy(strArray* sa);
typedef struct vcfData vcfData;
typedef struct paramStruct paramStruct;
typedef struct outfile_t outfile_t;
/* END-OF-FORWARD-DECLARATIONS ---------------------------------------------- */
/* MACROS ------------------------------------------------------------------- */
/* END-OF-MACROS ------------------------------------------------------------ */
/* TYPEDEF-STRUCTS ---------------------------------------------------------- */
/// @brief bblocks_t - structure for storing block bootstrapping blocks
/// @note positions: 0-based, [start, end)
struct bblocks_t {
/// @var n_blocks - number of blocks
size_t n_blocks;
/// @var n_contigs - number of contigs
size_t n_contigs;
/// @var n_ind - number of individuals
size_t n_ind;
/// \def rblocks[nReps][n_blocks] = size_t index of the sampled block
size_t** rblocks;
/// @var nsites_per_block[n_blocks]
/// nsites_per_block[i] == number of sites in block i
uint64_t* nsites_per_block;
strArray* contig_names;
/// @var block_start_pos[n_blocks]
/// block_start_pos[i] == position (vcfd->rec->pos) of the start of block i
/// @note 0-based, inclusive [start
size_t* block_start_pos;
/// @var block_end_pos[n_blocks]
/// block_end_pos[i] == position (vcfd->rec->pos) of the end of block i
/// @note 0-based, exclusive end)
size_t* block_end_pos;
/// @var block_contig[n_blocks]
/// block_contig[i] == index of the contig (in contig_names) that block i belongs to
size_t* block_contig;
/// @var block_start_siteidx[n_blocks]
/// block_start_siteidx[i] == index of the first site that belongs to block i
/// @note site index refers to the set of sites the program did not skip and are included in the analysis
/// if all sites from all contigs are used, this set is of size for(c in contigs) size+=contignsites[c]
/// the max siteidx is ((vcfd->nSites)-1), the min is 0, and it is global through all contigs
/// vcfd->nSites==pars->nSites
/// this information is collected during sites reading
/// @note 0-based siteidx inclusive [start
/// @note block_end = (wb == nBlocks - 1) ? max_nsites : block_start_siteidx[wb + 1];
size_t* block_start_siteidx;
};
/* END-OF-TYPEDEF-STRUCTS --------------------------------------------------- */
/* FUNCTION-DECLARATIONS ----------------------------------------------------- */
/// @brief bblocks_sample_with_replacement - perform the block bootstrapping sampling with replacement
/// @details
/// sample the blocks with replacement for all individuals as to preserve the correlation structure
void bblocks_sample_with_replacement(bblocks_t* bblocks);
void bblocks_print_bootstrap_samples(bblocks_t* bblocks, outfile_t* outfile);
void bblocks_print_blocks_tab(bblocks_t* bblocks, outfile_t* outfile);
bblocks_t* bblocks_init(void);
void bblocks_destroy(bblocks_t* bblocks);
void bblocks_get(bblocks_t* bblocks, vcfData* vcfd, paramStruct* pars);
/* END-OF-FUNCTION-DECLARATIONS ---------------------------------------------- */
#endif // __BOOTSTRAP_H__