minisp.h

#ifndef MINISP_H
#define MINISP_H

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

#define MSP_VERSION "0.4-r118"

typedef enum { MSP_FT_FASTX, MSP_FT_LINE } msp_ft_t;

typedef const char *msp_cstr_t;

typedef struct {
	msp_ft_t type;
	void *fp;
	void *buf;
} msp_file_t;

typedef struct {
	int32_t n, m;
	char **a;
	void *h;
} msp_strmap_t;

typedef struct {
	int64_t st, en;
} msp_blk1_t;

typedef struct {
	int64_t st, en;
	int64_t st2, en2; // thickStart and thickEnd
	int32_t cid, score, strand;
	int32_t n_blk;
	char *ctg, *name;
	msp_blk1_t blk[];
} msp_bed1_t;

typedef struct {
	int64_t n, off;
} msp_bedctg_t;

typedef struct {
	int64_t n, m;
	msp_bed1_t **a;
	msp_bedctg_t *c;
	msp_strmap_t *h;
} msp_bed_t;

typedef struct { // training data
	int32_t cid;
	uint64_t x; // pos<<3 | rev<<2 | acceptor<<1 | pos
	uint8_t *seq;
} msp_tdata1_t;

typedef struct {
	int64_t len;
	int64_t n[2], m[2];
	msp_tdata1_t *a[2];
} msp_tdata_t;

typedef struct { // simplified training data
	uint32_t label;
	uint8_t *seq;
	char *ctg; // allocated together with seq
} msp_sdata1_t;

typedef struct {
	int32_t len;
	uint32_t n_label;
	int64_t n, m;
	msp_sdata1_t *a;
} msp_sdata_t;

typedef struct { // prediction data
	uint64_t x;
	float f;
	int32_t s;
} msp_pdata1_t;

typedef struct {
	int64_t n, m;
	msp_pdata1_t *a;
} msp_pdata_t;

typedef struct { // accuracy statistics in each bin
	int64_t mt, mp; // marginal total, marginal positives
	int64_t tp, fp, tn, fn; // derived from mt and mp
	double spsc; // also derived
} msp_evalbin_t;

typedef struct {
	float step;
	int32_t n_bin;
	int64_t tot_t, tot_p;
	msp_evalbin_t bin[];
} msp_eval_t;

extern int msp_verbose;

#ifdef __cplusplus
extern "C" {
#endif

void msp_file_close(msp_file_t *f);

// training data
msp_tdata_t *msp_gen_train(const msp_bed_t *bed, msp_file_t *fx, int32_t ext, double frac_pos);
void msp_tdata_dump(FILE *fp, const msp_bed_t *bed, const msp_tdata_t *d);
void msp_tdata_destroy(msp_tdata_t *d);
msp_sdata_t *msp_sdata_read(const char *fn);
void msp_sdata_destroy(msp_sdata_t *d);

// FASTX reader
msp_file_t *msp_fastx_open(const char *fn);
int64_t msp_fastx_read(msp_file_t *fp, msp_cstr_t *name, msp_cstr_t *seq);

// BED reader
msp_file_t *msp_bed_open(const char *fn);
msp_bed_t *msp_bed_read(const char *fn);
void msp_bed_sort(msp_bed_t *bed);
void msp_bed_idxctg(msp_bed_t *bed);
int msp_bed_read1(msp_file_t *fp, msp_bed1_t **b_);
void msp_bed_destroy(msp_bed_t *bed);

// calibration data
msp_eval_t *msp_eval_init(float step);
msp_eval_t *msp_eval_read(const char *fn);
void msp_eval_update(msp_eval_t *e);

// strmap
msp_strmap_t *msp_strmap_init(void);
void msp_strmap_destroy(msp_strmap_t *m);
int32_t msp_strmap_add(msp_strmap_t *m, const char *s);
int32_t msp_strmap_get(const msp_strmap_t *m, const char *s);

#ifdef __cplusplus
}
#endif

#endif