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https://github.com/lh3/minimap2.git
synced 2026-10-02 14:38:13 +08:00
r367: index reader optionally writes index
This commit is contained in:
Heng Li
@@ -25,21 +25,16 @@
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extern "C" {
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#endif
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typedef struct {
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uint64_t x, y;
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} mm128_t;
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// hidden structures
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struct mm_idx_bucket_s;
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struct mm_bseq_file_s;
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struct mm_tbuf_s;
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// emulate 128-bit integers and arrays
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typedef struct { uint64_t x, y; } mm128_t;
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typedef struct { size_t n, m; mm128_t *a; } mm128_v;
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typedef struct { size_t n, m; uint64_t *a; } uint64_v;
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typedef struct { size_t n, m; uint32_t *a; } uint32_v;
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typedef struct {
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mm128_v a; // (minimizer, position) array
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int32_t n; // size of the _p_ array
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uint64_t *p; // position array for minimizers appearing >1 times
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void *h; // hash table indexing _p_ and minimizers appearing once
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} mm_idx_bucket_t;
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// minimap2 index
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typedef struct {
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char *name; // name of the db sequence
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uint64_t offset; // offset in mm_idx_t::S
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@@ -48,43 +43,50 @@ typedef struct {
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typedef struct {
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int32_t b, w, k, is_hpc;
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uint32_t n_seq; // number of reference sequences
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mm_idx_seq_t *seq; // sequence name, length and offset
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uint32_t *S; // 4-bit packed sequence
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mm_idx_bucket_t *B; // index
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uint32_t n_seq; // number of reference sequences
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mm_idx_seq_t *seq; // sequence name, length and offset
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uint32_t *S; // 4-bit packed sequence
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struct mm_idx_bucket_s *B; // index (hidden)
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void *km;
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} mm_idx_t;
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// minimap2 alignment
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typedef struct {
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uint32_t capacity;
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int32_t dp_score, dp_max, dp_max2;
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uint32_t blen;
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uint32_t n_diff;
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uint32_t n_ambi:30, trans_strand:2;
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uint32_t n_cigar;
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uint32_t capacity; // the capacity of cigar[]
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int32_t dp_score, dp_max, dp_max2; // DP score; score of the max-scoring segment; score of the best alternate mappings
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uint32_t blen; // block length
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uint32_t n_diff; // number of differences, including ambiguous bases
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uint32_t n_ambi:30, trans_strand:2; // number of ambiguous bases; transcript strand: 0 for unknown, 1 for +, 2 for -
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uint32_t n_cigar; // number of cigar operations in cigar[]
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uint32_t cigar[];
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} mm_extra_t;
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typedef struct {
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int32_t id;
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uint32_t cnt:31, rev:1;
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uint32_t rid:31, inv:1;
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int32_t score;
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int32_t qs, qe, rs, re;
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int32_t parent, subsc;
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int32_t as;
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int32_t fuzzy_mlen, fuzzy_blen;
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uint32_t mapq:8, split:2, sam_pri:1, n_sub:21; // TODO: n_sub is not used for now
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int32_t id; // ID for internal uses (see also parent below)
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uint32_t cnt:31, rev:1; // number of minimizers; if on the reverse strand
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uint32_t rid:31, inv:1; // reference index; if this is an alignment from inversion rescue
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int32_t score; // DP alignment score
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int32_t qs, qe, rs, re; // query start and end; reference start and end
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int32_t parent, subsc; // parent==id if primary; best alternate mapping score
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int32_t as; // offset in the a[] array (for internal uses only)
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int32_t fuzzy_mlen, fuzzy_blen; // seeded exact match length; seeded alignment block length (approximate)
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uint32_t mapq:8, split:2, sam_pri:1, n_sub:21; // mapQ; split pattern; if SAM primary; number of suboptimal mappings
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mm_extra_t *p;
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} mm_reg1_t;
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// indexing and mapping options
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typedef struct {
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float max_occ_frac;
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float mid_occ_frac;
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int sdust_thres; // score threshold for SDUST; 0 to disable
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int flag; // see MM_F_* macros
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short k, w, is_hpc, bucket_bits;
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int mini_batch_size;
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uint64_t batch_size;
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} mm_idxopt_t;
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int bw; // bandwidth
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typedef struct {
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float mid_occ_frac;
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int sdust_thres; // score threshold for SDUST; 0 to disable
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int flag; // see MM_F_* macros
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int bw; // bandwidth
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int max_gap, max_gap_ref; // break a chain if there are no minimizers in a max_gap window
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int max_chain_skip;
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int min_cnt;
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@@ -104,63 +106,44 @@ typedef struct {
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int min_ksw_len;
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int mini_batch_size;
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int32_t max_occ, mid_occ;
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int32_t mid_occ;
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} mm_mapopt_t;
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typedef struct {
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short k, w, is_hpc, bucket_bits;
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int mini_batch_size;
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uint64_t batch_size;
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} mm_idxopt_t;
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struct mm_bseq_file_s;
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// index reader
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typedef struct {
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int is_idx, n_parts;
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mm_idxopt_t opt;
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FILE *fp_out;
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union {
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struct mm_bseq_file_s *seq;
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FILE *idx;
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} fp;
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} mm_idx_reader_t;
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extern int mm_verbose, mm_dbg_flag;
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extern double mm_realtime0;
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struct mm_tbuf_s;
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// memory buffer for thread-local storage during mapping
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typedef struct mm_tbuf_s mm_tbuf_t;
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#define mm_seq4_set(s, i, c) ((s)[(i)>>3] |= (uint32_t)(c) << (((i)&7)<<2))
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#define mm_seq4_get(s, i) ((s)[(i)>>3] >> (((i)&7)<<2) & 0xf)
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// global variables
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extern int mm_verbose, mm_dbg_flag; // verbose level: 0 for no info, 1 for error, 2 for warning, 3 for message (default); debugging flag
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extern double mm_realtime0; // wall-clock timer
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void mm_idxopt_init(mm_idxopt_t *opt);
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void mm_mapopt_init(mm_mapopt_t *opt);
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int mm_preset(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo);
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int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo);
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void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi);
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mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt);
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int mm_idx_reader_is_idx(const mm_idx_reader_t *r);
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mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt, const char *fn_out);
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mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads);
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void mm_idx_reader_close(mm_idx_reader_t *r);
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void mm_idx_stat(const mm_idx_t *idx);
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int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
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void mm_idx_destroy(mm_idx_t *mi);
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// minimizer indexing
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void mm_idx_stat(const mm_idx_t *idx);
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const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);
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int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
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// minimizer index I/O
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void mm_idx_dump(FILE *fp, const mm_idx_t *mi);
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mm_idx_t *mm_idx_load(FILE *fp);
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// mapping
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mm_tbuf_t *mm_tbuf_init(void);
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void mm_tbuf_destroy(mm_tbuf_t *b);
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mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name);
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int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int n_threads);
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// obsolete APIs (for backward compatibility)
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// deprecated APIs for backward compatibility
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void mm_mapopt_init(mm_mapopt_t *opt);
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mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads);
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#ifdef __cplusplus
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