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Searched refs:chn_pen_gap (Results 1 – 3 of 3) sorted by relevance

/dports/biology/minimap2/minimap2-2.24/
H A Dlchain.c113 …mm128_t *aj, int32_t max_dist_x, int32_t max_dist_y, int32_t bw, float chn_pen_gap, float chn_pen_… in comput_sc() argument
129 lin_pen = chn_pen_gap * (float)dd + chn_pen_skip * (float)dg; in comput_sc()
148 …_y, int bw, int max_skip, int max_iter, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_… in mg_lchain_dp() argument
176 …sc = comput_sc(&a[i], &a[j], max_dist_x, max_dist_y, bw, chn_pen_gap, chn_pen_skip, is_cdna, n_seg… in mg_lchain_dp()
198 …tmp = comput_sc(&a[i], &a[max_ii], max_dist_x, max_dist_y, bw, chn_pen_gap, chn_pen_skip, is_cdna,… in mg_lchain_dp()
232 static inline int32_t comput_sc_simple(const mm128_t *ai, const mm128_t *aj, float chn_pen_gap, flo… in KRMQ_INIT()
243 lin_pen = chn_pen_gap * (float)dd + chn_pen_skip * (float)dg; in KRMQ_INIT()
250 …bw, int max_chn_skip, int cap_rmq_size, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_… in mg_lchain_rmq() argument
284 …q->y = (int32_t)a[j].y, q->i = j, q->pri = -(f[j] + 0.5 * chn_pen_gap * ((int32_t)a[j].x + (int32_… in mg_lchain_rmq()
320 sc = f[j] + comput_sc_simple(&a[i], &a[j], chn_pen_gap, chn_pen_skip, &exact, &width); in mg_lchain_rmq()
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H A Dmmpriv.h84 …_y, int bw, int max_skip, int max_iter, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_…
86 …bw, int max_chn_skip, int cap_rmq_size, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_…
H A Dmap.c243 float chn_pen_gap, chn_pen_skip; in mm_map_frag() local
278 chn_pen_gap = opt->chain_gap_scale * 0.01 * mi->k; in mm_map_frag()
282 chn_pen_gap, chn_pen_skip, n_a, a, &n_regs0, &u, b->km); in mm_map_frag()
285 chn_pen_gap, chn_pen_skip, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km); in mm_map_frag()
296 chn_pen_gap, chn_pen_skip, n_a, a, &n_regs0, &u, b->km); in mm_map_frag()
319 chn_pen_gap, chn_pen_skip, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km); in mm_map_frag()