From 9e7247cff938b09fa7ae4ba78810f85497df2bb9 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 23 May 2021 21:00:15 -0400 Subject: [PATCH] sync python with recent changes --- python/cmappy.pxd | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/python/cmappy.pxd b/python/cmappy.pxd index 459b246..c864f55 100644 --- a/python/cmappy.pxd +++ b/python/cmappy.pxd @@ -13,7 +13,9 @@ cdef extern from "minimap.h": int64_t flag int seed int sdust_thres + int max_qlen + int bw int max_gap, max_gap_ref int max_frag_len @@ -21,14 +23,19 @@ cdef extern from "minimap.h": int min_cnt int min_chain_score float chain_gap_scale + int rmq_size_cap, rmq_inner_dist + float mask_level int mask_len float pri_ratio int best_n + int max_join_long, max_join_short int min_join_flank_sc float min_join_flank_ratio + float alt_drop + int a, b, q, e, q2, e2 int sc_ambi int noncan @@ -39,13 +46,16 @@ cdef extern from "minimap.h": 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 int64_t 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)