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176 lines (157 loc) · 6.26 KB
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#ifndef MINIBWA_H
#define MINIBWA_H
#include <stdint.h>
#define MB_VERSION "0.7-r424-dirty"
#define MB_F_PAF (0x1LL) // output in the PAF format
#define MB_F_NO_UNMAP (0x2LL) // output unmapped query sequences
#define MB_F_COPY_COMMENT (0x4LL) // copy FASTX comments to output
#define MB_F_PE (0x8LL) // paired-end mode
#define MB_F_LONG (0x10LL) // long-sequence mode
#define MB_F_EQX (0x20LL) // = in CIGAR
#define MB_F_NO_KALLOC (0x40LL) // disable kalloc
#define MB_F_NO_ALN (0x80LL) // skip base alignment
#define MB_F_PE_PREDEF (0x100LL) // use predefined PE
#define MB_F_WRITE_DS (0x200LL) // write ds:Z
#define MB_F_WRITE_CS (0x400LL) // write cs:Z
#define MB_F_WRITE_MD (0x800LL) // write MD:Z
#define MB_F_2ND_SEQ (0x1000LL) // in SAM, write SEQ for secondary alignments
#define MB_F_SUPP_SOFT (0x2000LL) // in SAM, use soft-clips for supplementary alignments
#define MB_F_ADAP (0x4000LL) // adaptive mode
#define MB_F_PRIMARY5 (0x8000LL) // for Hi-C
#define MB_F_NO_PAIRING (0x10000LL) // don't pair reads
#define MB_F_METH (0x20000LL) // methylation mode
#define MB_CIGAR_MATCH 0
#define MB_CIGAR_INS 1
#define MB_CIGAR_DEL 2
#define MB_CIGAR_N_SKIP 3
#define MB_CIGAR_SOFTCLIP 4
#define MB_CIGAR_HARDCLIP 5
#define MB_CIGAR_PADDING 6
#define MB_CIGAR_EQ_MATCH 7
#define MB_CIGAR_X_MISMATCH 8
#define MB_CIGAR_STR "MIDNSHP=XB"
typedef struct {
uint64_t flag;
// seeding options
int32_t min_len; // min seed length
int32_t max_sub_occ; // look for shorter seed if smem occ below this value
int32_t max_occ; // max interval occurrence
// general algorithm options
int32_t bw, bw_long; // bandwidth
int32_t max_gap; // break a chain if there are no seeds in a max_gap window
int32_t max_sr_len; // in the adaptive sr mode, treat reads longer than this as long reads
// chaining options
int32_t
ABB2
max_chain_skip;
int32_t max_chain_iter;
int32_t min_chain_score; // min chaining score
float chain_gap_scale;
// hit processing options
float mask_level;
int32_t mask_len;
float pri_ratio;
int32_t best_n;
// alignment options
int32_t a, b; // match, mismatch
int32_t b_ts; // transition mismatch
int32_t b_ambi; // ambiguous mismatch
int32_t q, q2; // gap open, long gap open
int32_t e, e2; // gap extension, long gap extension
int32_t end_bonus;
int32_t min_dp_max; // min_dp_max*a is the min score
int32_t zdrop;
int32_t zdrop_inv;
int32_t min_ksw_len;
// pairing options
int32_t max_pe_ins;
int32_t max_rescue;
int32_t pen_unpair;
int32_t pe_avg, pe_std, pe_lo, pe_hi;
// input/output options
int32_t sb_len; // number of bases for batch smem
int32_t sb_seq; // number of sequences for batch smem
int32_t n_thread; // number of worker threads, excluding I/O threads
int32_t out_n; // max number of secondary alignments to output
float out_s;
int32_t seed;
int32_t xa_max;
int64_t mb_size; // mini-batch size
int64_t max_mb_size;
int64_t max_sw_mat;
int64_t cap_kalloc;
} mb_opt_t;
struct mb_idx_s;
typedef struct mb_idx_s mb_idx_t;
typedef struct {
uint32_t cap; // the capacity of cigar[]
int32_t dp_score, dp_max0; // DP score; score of the max-scoring segment
int32_t dp_max, dp_max2; // adjusted score and second best score for mapQ
uint32_t n_ambi:31, cs:1; // number of ambiguous bases;
int32_t n_cigar; // number of cigar operations in cigar[]
uint32_t cigar[]; // cs/MD is appended at the end
} mb_extra_t;
#define MB_PARENT_UNSET (-1)
#define MB_PARENT_TMP_PRI (-2)
typedef struct {
int64_t tid; // target ID (the original tid, NOT stranded)
int64_t ts, te; // target start and end
int32_t id; // ID for internal uses
int32_t cnt; // number of anchors
int32_t score, score0; // chaining score; score0 is the original chaining score
int32_t as; // offset in the a[] array (for internal uses only)
int32_t qs, qe; // query start and end
int32_t parent, n_sub, subsc;
int32_t mlen, blen;
int32_t mapq;
uint32_t hash;
uint32_t rev:1, proper_pair:1, sam_pri:1, flt:1, inv:1, split:2, split_inv:1, rescued:1, frac_high:8, seed_ratio:8, dummy:7;
mb_extra_t *p;
} mb_hit_t;
struct mb_tbuf_s;
typedef struct mb_tbuf_s mb_tbuf_t;
#ifdef __cplusplus
extern "C" {
#endif
mb_idx_t *mb_idx_load(const char *prefix, int32_t is_meth);
mb_idx_t *mb_idx_load_mmap(const char *prefix, int32_t is_meth, int preload);
void mb_idx_destroy(mb_idx_t *idx);
const char *mb_idx_ctg_name(const mb_idx_t *idx, int32_t tid);
int64_t mb_idx_ctg_len(const mb_idx_t *idx, int32_t tid);
void mb_opt_init(mb_opt_t *opt);
int mb_opt_preset(mb_opt_t *opt, const char *preset);
mb_tbuf_t *mb_tbuf_init(int no_kalloc);
void mb_tbuf_destroy(mb_tbuf_t *b);
int32_t mb_tbuf_reset(mb_tbuf_t *b, int64_t max_block_size);
/**
* Align one sequence
*
* @param opt options, typically initialized by mb_opt_init()
* @param idx index
* @param qlen query length
* @param seq query sequence, ASCII or 01/2/3 encoded
* @param mt methylation type: 0 for unmethylated, 1 for read1 (C-to-T) and 2 for read2 (G-to-A)
* @param n_hit (out) number of hits
* @param b thread buffer; can be NULL
* @param qname query name
*
* @return hit array
*/
mb_hit_t *mb_map(const mb_opt_t *opt, const mb_idx_t *idx, int32_t qlen, const char *seq, int32_t mt, int32_t *n_hit, mb_tbuf_t *b, const char *qname);
/**
* Align a set of sequences in batch
*
* @param opt options, typically initialized by mb_opt_init()
* @param idx index
* @param n_seq number of sequences
* @param qlen query lengths, of size n_seq
* @param seq query sequences, ASCII or 01/2/3 encoded, of size n_seq
* @param n_hit (out) number of hits, of size n_seq
* @param b thread buffer; can be NULL
* @param qname query name, of size n_seq
*
* @return hits, of size n_seq
*/
mb_hit_t **mb_map_batch(const mb_opt_t *opt, const mb_idx_t *idx, int32_t n_seq, const int32_t *qlen, const char **seq, int32_t *n_hit, mb_tbuf_t *b, const char **qname);
#ifdef __cplusplus
}
#endif
#endif