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r1049: removed the long-join heuristics

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Heng Li
2021-05-24 16:21:40 -04:00
parent 4f91558160
commit 379728726a
7 changed files with 5 additions and 78 deletions
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map.c
+1 -3
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@@ -210,8 +210,6 @@ static void chain_post(const mm_mapopt_t *opt, int max_chain_gap_ref, const mm_i
mm_set_parent(km, opt->mask_level, opt->mask_len, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, max_chain_gap_ref, mi->k*2, opt->best_n, n_segs, qlens, n_regs, regs);
if (!(opt->flag & (MM_F_SPLICE|MM_F_SR|MM_F_NO_LJOIN))) // long join not working well without primary chains
mm_join_long(km, opt, qlen, n_regs, regs, a);
}
}
@@ -302,7 +300,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
a = mg_lchain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score,
opt->chain_gap_scale * 0.01 * mi->k, 0.0f, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
}
} else if (opt->bw_long > opt->bw && !(opt->flag & MM_F_RMQ) && n_segs == 1 && n_regs0 > 1) {
} else if (opt->bw_long > opt->bw && !(opt->flag & (MM_F_RMQ|MM_F_NO_LJOIN)) && n_segs == 1 && n_regs0 > 1) {
int32_t st = (int32_t)a[0].y, en = (int32_t)a[(int32_t)u[0] - 1].y;
if (qlen_sum - (en - st) > 1000 || en - st > qlen_sum * .1) {
int32_t i;