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dev-r1079: per-read error rate

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more tuning needed
This commit is contained in:
Heng Li
2021-07-18 20:38:53 -04:00
parent 8a6edab847
commit 161ae7ff73
6 changed files with 85 additions and 34 deletions
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options.c
+5 -8
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@@ -43,7 +43,6 @@ 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;
@@ -54,6 +53,9 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->mini_batch_size = 500000000;
opt->max_sw_mat = 100000000;
opt->rank_min_len = 500;
opt->rank_frac = 0.9f;
opt->pe_ori = 0; // FF
opt->pe_bonus = 33;
}
@@ -69,11 +71,6 @@ 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);
}
@@ -131,7 +128,7 @@ 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->b2 = 0;
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 24, mo->e2 = 1;
mo->zdrop = mo->zdrop_inv = 100;
mo->end_bonus = 10;
mo->max_frag_len = 800;
@@ -150,7 +147,7 @@ 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->b2 = 0;
mo->a = 1, mo->b = 2, mo->q = 2, mo->e = 1, mo->q2 = 32, mo->e2 = 0;
mo->noncan = 9;
mo->junc_bonus = 9;
mo->zdrop = 200, mo->zdrop_inv = 100; // because mo->a is halved