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add new options for ont assembly

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chhylp123
2025-03-18 12:29:48 -04:00
parent b3b18ab1d0
commit ec9a8b222d
3 changed files with 38 additions and 2 deletions
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htab.cpp
+17 -1
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@@ -546,6 +546,21 @@ const int ha_pt_cnt(const ha_pt_t *h, uint64_t hash)
return kh_key(g->h, k) & YAK_MAX_COUNT;
}
inline uint64_t flt_quals(char *sc_a, uint64_t sc_l, uint64_t sc_off, int64_t sc_cut)
{
int64_t sc_min = sc_l * sc_cut, sc_tot; uint64_t k;
for (k = sc_tot = 0; (k < sc_l) && (sc_tot < sc_min); k++) {
sc_tot += (((uint8_t)sc_a[k]) - sc_off);
}
// if(sc_tot < sc_min) {
// fprintf(stderr, "[M::%s] sc_tot::%ld, sc_min::%ld, sc_l::%lu\n", __func__, sc_tot, sc_min, sc_l);
// }
if(sc_tot < sc_min) return 0;
return 1;
}
/**********************************
* Buffer for counting all k-mers *
**********************************/
@@ -745,7 +760,8 @@ static void *sf##_worker_count(void *data, int step, void *in) /** callback for
} else {\
while ((ret = kseq_read(p->ks)) >= 0) {\
int l = (int)(p->ks->seq.l) - (int)(p->opt->adaLen) - (int)(p->opt->adaLen);\
if(l <= 0) continue;\
if((l <= 0) || (l < asm_opt.rl_cut)) continue;\
if((asm_opt.is_sc) && (asm_opt.sc_cut > 0) && (!flt_quals(p->ks->qual.s+p->opt->adaLen, l, 33, asm_opt.sc_cut))) continue;\
if (p->n_seq >= 1<<28) {\
fprintf(stderr, "ERROR: this implementation supports no more than %d reads\n", 1<<28);\
exit(1);\