partig.h

#ifndef PARTIG_H
#define PARTIG_H

#include <stdint.h>
#include <stdio.h>
#include "gfa.h"

#define PT_VERSION "0.0.0-dirty"

typedef struct {
	uint64_t x, y;
} pt128_t;

typedef struct {
	uint64_t x;
	uint64_t rid:28, pos:27, rev:1, span:8;
} pt_mz1_t;

typedef struct { uint32_t n, m; pt128_t *a; } pt128_v;
typedef struct { uint32_t n, m; pt_mz1_t *a; } pt_mz1_v;

typedef struct {
	int32_t k, w, is_hpc;
	int32_t max_occ;
	int32_t min_cnt;
	double min_sim, diff_thres;
} pt_pdopt_t;

typedef struct {
	int32_t topn;
	int32_t n_perturb;
	uint64_t seed;
	double f_perturb;
} pt_svopt_t;

typedef struct {
	uint32_t sid[2], m, rev;
	double sim;
} pt_match1_t;

typedef struct {
	uint32_t cnt2, cnt1;
} pt_uinfo_t;

typedef struct {
	uint32_t n_seg; // number of segments; same as gfa_t::n_seg
	uint32_t n_ma; // size of the ma[] array below
	uint64_t *idx; // index into ma[] (of size n_seg)
	pt_uinfo_t *info; // of size n_seg
	pt_match1_t *ma;
} pt_match_t;

extern uint32_t pt_verbose;

void pt_pdopt_init(pt_pdopt_t *opt);
void pt_svopt_init(pt_svopt_t *opt);

pt_match_t *pt_pdist(const pt_pdopt_t *opt, const gfa_t *g);
void pt_match_print(FILE *fp, const gfa_t *g, const pt_match_t *ma);
void pt_match_free(pt_match_t *ma);

double pt_cputime(void);
double pt_realtime(void);
long pt_peakrss(void);

#endif