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miniprot.h
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miniprot.h
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#ifndef MINIPROT_H
#define MINIPROT_H
#include <stdint.h>
#define MP_VERSION "0.13-r260-dirty"
#define MP_F_NO_SPLICE 0x1
#define MP_F_NO_ALIGN 0x2
#define MP_F_SHOW_UNMAP 0x4
#define MP_F_GFF 0x8
#define MP_F_NO_PAF 0x10
#define MP_F_GTF 0x20
#define MP_F_NO_PRE_CHAIN 0x40
#define MP_F_SHOW_RESIDUE 0x80
#define MP_F_SHOW_TRANS 0x100
#define MP_F_NO_CS 0x200
#define MP_FEAT_CDS 0
#define MP_FEAT_STOP 1
#define MP_BITS_PER_AA 4
#define MP_BLOCK_BONUS 2
#define MP_CODON_STD 1
#define MP_IDX_MAGIC "MPI\3"
#ifdef __cplusplus
extern "C" {
#endif
typedef struct { uint64_t x, y; } mp128_t;
typedef struct { int32_t n, m; mp128_t *a; } mp128_v;
typedef struct { int32_t n, m; uint64_t *a; } mp64_v;
typedef struct {
int32_t bbit; // block bit
int32_t min_aa_len; // ignore ORFs shorter than this
int32_t kmer, mod_bit;
uint32_t trans_code;
} mp_idxopt_t;
typedef struct {
uint32_t flag;
int64_t mini_batch_size;
int32_t max_occ;
int32_t max_gap; // max gap on the query protein, in aa
int32_t max_intron;
int32_t min_max_intron, max_max_intron;
int32_t bw; // bandwidth, in aa
int32_t max_ext;
int32_t max_ava;
int32_t min_chn_cnt;
int32_t max_chn_max_skip;
int32_t max_chn_iter;
int32_t min_chn_sc;
float chn_coef_log;
float mask_level;
int32_t mask_len;
float pri_ratio;
float out_sim, out_cov;
int32_t best_n, out_n;
int32_t kmer2;
int32_t go, ge, io, fs; // gap open, extension, intron open, and frame-shift/stop-codon
int32_t io_end;
float ie_coef;
int32_t sp_model;
float sp_scale;
int32_t xdrop;
int32_t end_bonus;
int32_t asize; // size of the alphabet; always 22 in current implementation
int32_t gff_delim;
int32_t max_intron_flank;
const char *gff_prefix;
int8_t mat[484];
} mp_mapopt_t;
typedef struct {
uint32_t n, m;
uint64_t *a; // pos<<56 | score<<1 | acceptor
} mp_spsc_t;
typedef struct {
int64_t off, len;
char *name;
} mp_ctg_t;
typedef struct {
int32_t n_ctg, m_ctg;
int32_t l_name;
int64_t l_seq, m_seq;
uint8_t *seq; // TODO: separate this into multiple blocks; low priority
mp_ctg_t *ctg;
char *name;
void *h; // hash table to map sequence name to cid
mp_spsc_t *spsc; // of size n_ctg*2
} mp_ntdb_t;
typedef struct {
mp_idxopt_t opt;
uint32_t n_block;
mp_ntdb_t *nt;
int64_t n_kb, *ki;
uint32_t *bo, *kb;
} mp_idx_t;
typedef struct {
int32_t dp_score, dp_max, dp_max2;
int32_t n_cigar, m_cigar;
int32_t blen; // CDS length in alignment
int32_t n_fs; // number of frameshift events
int32_t n_stop; // number of in-frame stop codons
int32_t dist_stop; // distance in bp to the closest stop codon
int32_t dist_start; // distance in bp the the closest 'M'
int32_t n_iden, n_plus;
uint32_t cigar[];
} mp_extra_t;
typedef struct {
int64_t vs, ve;
int32_t qs, qe;
int16_t type, phase;
int32_t n_fs, n_stop;
int32_t score, n_iden, blen;
char donor[2], acceptor[2];
} mp_feat_t;
typedef struct {
int32_t off, cnt;
int32_t id, parent;
int32_t n_sub, subsc;
int32_t n_feat, m_feat, n_exon;
int32_t chn_sc;
int32_t chn_sc_ungap;
uint32_t hash;
uint32_t vid; // cid<<1 | rev
int32_t qs, qe;
int64_t vs, ve;
uint64_t *a;
mp_feat_t *feat;
mp_extra_t *p;
} mp_reg1_t;
struct mp_tbuf_s;
typedef struct mp_tbuf_s mp_tbuf_t;
extern int32_t mp_verbose, mp_dbg_flag;
extern char *ns_tab_nt_i2c, *ns_tab_aa_i2c;
extern uint8_t ns_tab_a2r[22], ns_tab_nt4[256], ns_tab_aa20[256], ns_tab_aa13[256];
extern uint8_t ns_tab_codon[64], ns_tab_codon13[64];
void mp_start(void);
void mp_idxopt_init(mp_idxopt_t *io);
void mp_mapopt_init(mp_mapopt_t *mo);
void mp_mapopt_set_fs(mp_mapopt_t *mo, int32_t fs);
void mp_mapopt_set_max_intron(mp_mapopt_t *mo, int64_t gsize);
int32_t mp_mapopt_check(const mp_mapopt_t *mo);
mp_idx_t *mp_idx_load(const char *fn, const mp_idxopt_t *io, int32_t n_threads);
void mp_idx_destroy(mp_idx_t *mi);
int mp_idx_dump(const char *fn, const mp_idx_t *mi);
mp_idx_t *mp_idx_restore(const char *fn);
void mp_idx_print_stat(const mp_idx_t *mi, int32_t max_occ);
int32_t mp_ntseq_read_spsc(mp_ntdb_t *nt, const char *fn, int32_t max_sc);
int32_t mp_map_file(const mp_idx_t *idx, const char *fn, const mp_mapopt_t *opt, int n_threads);
#ifdef __cplusplus
}
#endif
#endif