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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
int 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
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 mask_level
float pri_ratio
int best_n
int max_join_long, max_join_short
int min_join_flank_sc
float min_join_flank_ratio
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 pe_ori, pe_bonus
float mid_occ_frac
int32_t min_mid_occ
int32_t mid_occ
int32_t max_occ
int mini_batch_size
int64_t max_sw_mat
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()
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