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sync python with recent changes

This commit is contained in:
Heng Li 2021-05-23 21:00:15 -04:00
parent f97008a10e
commit 9e7247cff9
1 changed files with 10 additions and 0 deletions
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python/cmappy.pxd
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@ -13,7 +13,9 @@ cdef extern from "minimap.h":
int64_t flag int64_t flag
int seed int seed
int sdust_thres int sdust_thres
int max_qlen int max_qlen
int bw int bw
int max_gap, max_gap_ref int max_gap, max_gap_ref
int max_frag_len int max_frag_len
@ -21,14 +23,19 @@ cdef extern from "minimap.h":
int min_cnt int min_cnt
int min_chain_score int min_chain_score
float chain_gap_scale float chain_gap_scale
int rmq_size_cap, rmq_inner_dist
float mask_level float mask_level
int mask_len int mask_len
float pri_ratio float pri_ratio
int best_n int best_n
int max_join_long, max_join_short int max_join_long, max_join_short
int min_join_flank_sc int min_join_flank_sc
float min_join_flank_ratio float min_join_flank_ratio
float alt_drop float alt_drop
int a, b, q, e, q2, e2 int a, b, q, e, q2, e2
int sc_ambi int sc_ambi
int noncan int noncan
@ -39,13 +46,16 @@ cdef extern from "minimap.h":
int min_ksw_len int min_ksw_len
int anchor_ext_len, anchor_ext_shift int anchor_ext_len, anchor_ext_shift
float max_clip_ratio float max_clip_ratio
int pe_ori, pe_bonus int pe_ori, pe_bonus
float mid_occ_frac float mid_occ_frac
int32_t min_mid_occ int32_t min_mid_occ
int32_t mid_occ int32_t mid_occ
int32_t max_occ int32_t max_occ
int64_t mini_batch_size int64_t mini_batch_size
int64_t max_sw_mat int64_t max_sw_mat
const char *split_prefix const char *split_prefix
int mm_set_opt(char *preset, mm_idxopt_t *io, mm_mapopt_t *mo) int mm_set_opt(char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)