from libc.stdint cimport int8_t, uint8_t, int32_t, int64_t, uint32_t, uint64_t cdef extern from "minimap.h": # # Options # ctypedef struct mm_idxopt_t: short k, w, flag, bucket_bits int64_t mini_batch_size uint64_t batch_size ctypedef struct mm_mapopt_t: int64_t flag int seed int sdust_thres int max_qlen int bw, bw_long int max_gap, max_gap_ref int max_frag_len int max_chain_skip, max_chain_iter int min_cnt int min_chain_score float chain_gap_scale float chain_skip_scale int rmq_size_cap, rmq_inner_dist int rmq_rescue_size float rmq_rescue_ratio float mask_level int mask_len float pri_ratio int best_n float alt_drop int a, b, q, e, q2, e2 int sc_ambi int noncan int junc_bonus int zdrop, zdrop_inv int end_bonus int min_dp_max int min_ksw_len int anchor_ext_len, anchor_ext_shift float max_clip_ratio int rank_min_len float rank_frac int pe_ori, pe_bonus float mid_occ_frac float q_occ_frac int32_t min_mid_occ int32_t mid_occ int32_t max_occ int64_t mini_batch_size int64_t max_sw_mat int64_t cap_kalloc const char *split_prefix int mm_set_opt(char *preset, mm_idxopt_t *io, mm_mapopt_t *mo) int mm_verbose # # Indexing # ctypedef struct mm_idx_seq_t: char *name uint64_t offset uint32_t len ctypedef struct mm_idx_bucket_t: pass ctypedef struct mm_idx_t: int32_t b, w, k, flag uint32_t n_seq mm_idx_seq_t *seq uint32_t *S mm_idx_bucket_t *B void *km void *h ctypedef struct mm_idx_reader_t: pass mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt, const char *fn_out) mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads) void mm_idx_reader_close(mm_idx_reader_t *r) void mm_idx_destroy(mm_idx_t *mi) void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi) int mm_idx_index_name(mm_idx_t *mi) # # Mapping (key struct defined in cmappy.h below) # ctypedef struct mm_reg1_t: pass ctypedef struct mm_tbuf_t: pass mm_tbuf_t *mm_tbuf_init() void mm_tbuf_destroy(mm_tbuf_t *b) void *mm_tbuf_get_km(mm_tbuf_t *b) int mm_gen_cs(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int no_iden) int mm_gen_MD(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq) # # Helper header (because it is hard to expose mm_reg1_t with Cython) # cdef extern from "cmappy.h": ctypedef struct mm_hitpy_t: const char *ctg int32_t ctg_start, ctg_end int32_t qry_start, qry_end int32_t blen, mlen, NM, ctg_len uint8_t mapq, is_primary int8_t strand, trans_strand int32_t seg_id int32_t n_cigar32 uint32_t *cigar32 void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h) void mm_free_reg1(mm_reg1_t *r) mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char *seq1, const char *seq2, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt) char *mappy_fetch_seq(const mm_idx_t *mi, const char *name, int st, int en, int *l) mm_idx_t *mappy_idx_seq(int w, int k, int is_hpc, int bucket_bits, const char *seq, int l) ctypedef struct kstring_t: unsigned l, m char *s ctypedef struct kstream_t: pass ctypedef struct kseq_t: kstring_t name, comment, seq, qual int last_char kstream_t *f kseq_t *mm_fastx_open(const char *fn) void mm_fastx_close(kseq_t *ks) int kseq_read(kseq_t *seq) char *mappy_revcomp(int l, const uint8_t *seq) int mm_verbose_level(int v) void mm_reset_timer()