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added two more filters

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This commit is contained in:
Heng Li
2019-12-24 00:06:44 -05:00
parent 43b0399991
commit de6ad4c1d9
4 changed files with 19 additions and 0 deletions
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4
main.c
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@@ -69,6 +69,8 @@ static ko_longopt_t long_options[] = {
{ "sam-hit-only", ko_no_argument, 342 },
{ "idx-min-occ", ko_required_argument, 343 },
{ "idx-max-occ", ko_required_argument, 344 },
{ "flt-max-dv", ko_required_argument, 345 },
{ "flt-min-blen", ko_required_argument, 346 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
@@ -214,6 +216,8 @@ int main(int argc, char *argv[])
else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
else if (c == 343) ipt.min_occ = mm_parse_num(o.arg); // --idx-min-occ
else if (c == 344) ipt.max_occ = mm_parse_num(o.arg); // --idx-max-occ
else if (c == 345) opt.flt_max_dv = atof(o.arg); // --flt-max-dv
else if (c == 346) opt.flt_min_blen = mm_parse_num(o.arg); // --flt-min-blen
else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary

9
map.c
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@@ -351,6 +351,15 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
chain_post(opt, max_chain_gap_ref, mi, b->km, qlen_sum, n_segs, qlens, &n_regs0, regs0, a);
if (!is_sr) mm_est_err(mi, qlen_sum, n_regs0, regs0, a, n_mini_pos, mini_pos);
if (!is_sr && n_segs == 1) {
for (i = j = 0; i < n_regs0; ++i) {
mm_reg1_t *r = &regs0[i];
if (r->div > opt->flt_max_dv) continue;
if (r->blen < opt->flt_min_blen) continue;
regs0[j++] = regs0[i];
}
n_regs0 = j;
}
if (n_segs == 1) { // uni-segment
regs0 = align_regs(opt, mi, b->km, qlens[0], seqs[0], &n_regs0, regs0, a);

3
minimap.h
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@@ -119,6 +119,9 @@ typedef struct {
int min_cnt; // min number of minimizers on each chain
int min_chain_score; // min chaining score
float flt_max_dv;
int flt_min_blen;
float mask_level;
float pri_ratio;
int best_n; // top best_n chains are subjected to DP alignment

3
options.c
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@@ -27,6 +27,9 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->max_chain_skip = 25;
opt->max_chain_iter = 5000;
opt->flt_max_dv = 1.0f;
opt->flt_min_blen = 0;
opt->mask_level = 0.5f;
opt->pri_ratio = 0.8f;
opt->best_n = 5;