yak.h

#ifndef YAK_H
#define YAK_H

#define YAKS_VERSION "0.1-r58-dirty"

#include <stdint.h>
#include <map>
#include <set>
#include <vector>

#define YAK_MAX_KMER     31
#define YAK_COUNTER_BITS 18

#define YAK_POS_ID_BITS 48
#define YAK_POS_BITS 32
#define YAK_POS_REPEAT_MASK (1<<(YAK_POS_ID_BITS-1))
#define YAK_POS_POS_MASK ((1<<(YAK_POS_BITS))-1)
#define YAK_POS_ID_MASK ((1<<(YAK_POS_ID_BITS))-1-YAK_POS_REPEAT_MASK-YAK_POS_POS_MASK)

#define YAK_N_COUNTS     (1<<YAK_COUNTER_BITS)
#define YAK_MAX_COUNT    ((1<<YAK_COUNTER_BITS)-1)
#define YAK_REPEAT_MASK    (1<<(YAK_COUNTER_BITS-1))
#define YAK_FORWARD_MASK    (1<<(YAK_COUNTER_BITS-2))
#define YAK_KEY_MASK    ((1<<YAK_COUNTER_BITS)- 1 - YAK_REPEAT_MASK - YAK_FORWARD_MASK)
#define YAK_POS_MASK    ((1<<30)- 1)

#define YAK_BLK_SHIFT  9 // 64 bytes, the size of a cache line
#define YAK_BLK_MASK   ((1<<(YAK_BLK_SHIFT)) - 1)

#define YAK_LOAD_ALL       1
#define YAK_LOAD_TRIOBIN1  2
#define YAK_LOAD_TRIOBIN2  3

#define YAK_MAGIC "YAK\2"

typedef struct {
	int32_t bf_shift, bf_n_hash;
	int32_t k;
	int32_t pre;
	int32_t n_thread;
	int64_t chunk_size;
} yak_copt_t;

typedef struct {
	int32_t print_each;
	int32_t min_len;
	int32_t n_threads;
	double min_frac;
	double fpr;
	int64_t chunk_size;
} yak_qopt_t;

typedef struct {
	int64_t tot;
	double qv_raw, qv, cov, err;
	double fpr_lower, fpr_upper;
	double adj_cnt[1<<YAK_COUNTER_BITS];
} yak_qstat_t;

typedef struct {
	int n_shift, n_hashes;
	uint8_t *b;
} yak_bf_t;

struct yak_ht_t;

typedef struct {
	struct yak_ht_t *h;
	yak_bf_t *b;
} yak_ch1_t;

typedef struct {
	int k, pre, n_hash, n_shift;
	uint64_t tot;
	yak_ch1_t *h;
} yak_ch_t;

typedef struct{
	int n_seq;
	char** names;
	yak_ch_t** yak_ch;
} yak_ch_arr_t;


typedef struct{
	bool repeated;
	bool init;
	uint16_t record;
} recordset1_t;

typedef struct{
	uint32_t current_length;
	recordset1_t *recordsets;
} recordset_t;

typedef struct{
	bool repeated;
	bool init;
	uint16_t uni_id;
	uint64_t pos;
} record_ps_t;

typedef struct{
	uint32_t current_length;
	record_ps_t *records;
} recordset_ps_t;

extern int yak_verbose;
extern unsigned char seq_nt4_table[256];

void yak_copt_init(yak_copt_t *opt);

yak_bf_t *yak_bf_init(int n_shift, int n_hashes);
void yak_bf_destroy(yak_bf_t *b);
int yak_bf_insert(yak_bf_t *b, uint64_t hash);

yak_ch_t *yak_ch_init(int k, int pre, int n_hash, int n_shift);
void yak_ch_destroy(yak_ch_t *h);
void yak_ch_destroy_bf(yak_ch_t *h);
int yak_ch_insert_list(yak_ch_t *h, int create_new, int n, const uint64_t *a);
int yak_ch_insert_list_kmer_record_mapping(yak_ch_t *h, int create_new, int n, const uint64_t *a, const bool *f, recordset_t* recordset, const uint16_t *r,  long i, std::set<uint64_t>* deleted);
int yak_ch_insert_list_kmer_pos(yak_ch_t *h, yak_ch_t *h_pos, int create_new, int n, const uint64_t *a, const uint16_t *r, const uint32_t*pos, long i);
int yak_ch_get(const yak_ch_t *h, uint64_t x);
int yak_ch_get_k(const yak_ch_t *h, uint64_t x);
uint16_t yak_ch_get_pos(const yak_ch_t *h, const yak_ch_t *h_pos, uint64_t x, uint32_t *pos);

void yak_ch_clear(yak_ch_t *h, int n_thread);
void yak_ch_hist(const yak_ch_t *h, int64_t cnt[YAK_N_COUNTS], int n_thread);
void yak_ch_shrink(yak_ch_t *h, int min, int max, int n_thread);
int yak_ch_dump(const yak_ch_t *h, const char *fn);
yak_ch_t *yak_ch_restore(const char *fn);
yak_ch_t *yak_ch_restore_core(yak_ch_t *ch0, const char *fn, int mode, ...);

yak_ch_t *yak_count(const char *fn, const yak_copt_t *opt, yak_ch_t *h0);
yak_ch_t *yak_count_create_new(const char *fn, const yak_copt_t *opt, yak_ch_t *h0);
yak_ch_arr_t* yak_count_multi(const char *fn, const yak_copt_t *opt, yak_ch_arr_t *h0);

void yak_qopt_init(yak_qopt_t *opt);
void yak_qv(const yak_qopt_t *opt, const char *fn, const yak_ch_t *ch, int64_t *cnt);
int yak_qv_solve(const int64_t *hist, const int64_t *cnt, int kmer, double fpr, yak_qstat_t *qs);

#endif