121 lines
2.5 KiB
Cython
121 lines
2.5 KiB
Cython
from libc.stdint cimport int8_t, uint8_t, int32_t, int64_t, uint32_t, uint64_t
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cdef extern from "minimap.h":
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#
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# Options
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#
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ctypedef struct mm_idxopt_t:
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short k, w, flag, bucket_bits
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int mini_batch_size
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uint64_t batch_size
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ctypedef struct mm_mapopt_t:
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int seed
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int sdust_thres
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int flag
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int bw
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int max_gap, max_gap_ref
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int max_frag_len
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int max_chain_skip
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int min_cnt
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int min_chain_score
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float mask_level
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float pri_ratio
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int best_n
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int max_join_long, max_join_short
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int min_join_flank_sc
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int a, b, q, e, q2, e2
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int noncan
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int zdrop
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int end_bonus
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int min_dp_max
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int min_ksw_len
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int min_end_match;
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int anchor_ext_len, anchor_ext_shift
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int pe_ori, pe_bonus
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float mid_occ_frac
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int32_t mid_occ
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int32_t max_occ
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int mini_batch_size
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int mm_set_opt(char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
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int mm_verbose
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#
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# Indexing
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#
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ctypedef struct mm_idx_seq_t:
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char *name
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uint64_t offset
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uint32_t len
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ctypedef struct mm_idx_bucket_t:
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pass
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ctypedef struct mm_idx_t:
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int32_t b, w, k, flag
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uint32_t n_seq
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mm_idx_seq_t *seq
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uint32_t *S
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mm_idx_bucket_t *B
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void *km
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ctypedef struct mm_idx_reader_t:
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pass
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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_destroy(mm_idx_t *mi)
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void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
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#
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# Mapping (key struct defined in cmappy.h below)
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#
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ctypedef struct mm_reg1_t:
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pass
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ctypedef struct mm_tbuf_t:
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pass
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mm_tbuf_t *mm_tbuf_init()
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void mm_tbuf_destroy(mm_tbuf_t *b)
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#
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# Helper header (because it is hard to expose mm_reg1_t with Cython)
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#
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cdef extern from "cmappy.h":
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ctypedef struct mm_hitpy_t:
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const char *ctg
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int32_t ctg_start, ctg_end
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int32_t qry_start, qry_end
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int32_t blen, mlen, NM, ctg_len
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uint8_t mapq, is_primary
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int8_t strand, trans_strand
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int32_t seg_id
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int32_t n_cigar32
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uint32_t *cigar32
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void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
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void mm_free_reg1(mm_reg1_t *r)
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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)
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ctypedef struct kstring_t:
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unsigned l, m
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char *s
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ctypedef struct kstream_t:
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pass
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ctypedef struct kseq_t:
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kstring_t name, comment, seq, qual
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int last_char
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kstream_t *f
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kseq_t *mm_fastx_open(const char *fn)
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void mm_fastx_close(kseq_t *ks)
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int kseq_read(kseq_t *seq)
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int mm_verbose_level(int v)
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void mm_reset_timer()
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