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r367: index reader optionally writes index

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This commit is contained in:
Heng Li
2017-09-14 21:18:13 -04:00
parent eb00521d9b
commit e2823d4aee
5 changed files with 83 additions and 90 deletions
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map.c
+6 -7
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@@ -11,7 +11,6 @@
void mm_mapopt_init(mm_mapopt_t *opt)
{
memset(opt, 0, sizeof(mm_mapopt_t));
opt->max_occ_frac = 1e-5f;
opt->mid_occ_frac = 2e-4f;
opt->sdust_thres = 0;
@@ -41,18 +40,18 @@ void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
{
if (opt->flag & MM_F_SPLICE_BOTH)
opt->flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV);
if (opt->max_occ <= 0)
opt->max_occ = mm_idx_cal_max_occ(mi, opt->max_occ_frac);
if (opt->mid_occ <= 0)
opt->mid_occ = mm_idx_cal_max_occ(mi, opt->mid_occ_frac);
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d; max_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0),
opt->mid_occ, opt->max_occ);
fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), opt->mid_occ);
}
int mm_preset(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
{
if (strcmp(preset, "ava-ont") == 0) {
if (preset == 0) {
mm_idxopt_init(io);
mm_mapopt_init(mo);
} else if (strcmp(preset, "ava-ont") == 0) {
io->is_hpc = 0, io->k = 15, io->w = 5;
mo->flag |= MM_F_AVA | MM_F_NO_SELF;
mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25;