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dev-r1078: decoupling ranking penalty

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Heng Li
2021-07-18 16:22:48 -04:00
parent 15118dd521
commit 8a6edab847
5 changed files with 23 additions and 17 deletions
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options.c
+8 -2
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@@ -43,6 +43,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->alt_drop = 0.15f;
opt->a = 2, opt->b = 4, opt->q = 4, opt->e = 2, opt->q2 = 24, opt->e2 = 1;
opt->b2 = 5;
opt->sc_ambi = 1;
opt->zdrop = 400, opt->zdrop_inv = 200;
opt->end_bonus = -1;
@@ -68,6 +69,11 @@ void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
if (opt->max_mid_occ > opt->min_mid_occ && opt->mid_occ > opt->max_mid_occ)
opt->mid_occ = opt->max_mid_occ;
}
if (opt->b2 > 0 && opt->b2 * opt->a < opt->b) {
opt->b2 = (int)opt->b / opt->a;
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s] addjusted the ranking penalty to %d\n", __func__, opt->b2);
}
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), opt->mid_occ);
}
@@ -125,7 +131,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
io->flag = 0, io->k = 21, io->w = 11;
mo->flag |= MM_F_SR | MM_F_FRAG_MODE | MM_F_NO_PRINT_2ND | MM_F_2_IO_THREADS | MM_F_HEAP_SORT;
mo->pe_ori = 0<<1|1; // FR
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 24, mo->e2 = 1;
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 24, mo->e2 = 1, mo->b2 = 0;
mo->zdrop = mo->zdrop_inv = 100;
mo->end_bonus = 10;
mo->max_frag_len = 800;
@@ -144,7 +150,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV | MM_F_SPLICE_FLANK;
mo->max_sw_mat = 0;
mo->max_gap = 2000, mo->max_gap_ref = mo->bw = mo->bw_long = 200000;
mo->a = 1, mo->b = 2, mo->q = 2, mo->e = 1, mo->q2 = 32, mo->e2 = 0;
mo->a = 1, mo->b = 2, mo->q = 2, mo->e = 1, mo->q2 = 32, mo->e2 = 0, mo->b2 = 0;
mo->noncan = 9;
mo->junc_bonus = 9;
mo->zdrop = 200, mo->zdrop_inv = 100; // because mo->a is halved