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r342-misjoin

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chhylp123
2021-06-19 14:09:09 -04:00
parent e3b721c29a
commit 5a400af39d
9 changed files with 845 additions and 22 deletions
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hic.cpp
+40 -9
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@@ -2100,13 +2100,26 @@ void print_hits(ha_ug_index* idx, kvec_pe_hit* hits, const enzyme *fn1, const en
destory_reads(&r1);
}
void print_hits_simp(ha_ug_index* idx, kvec_pe_hit* hits)
{
uint64_t k, shif = 64 - idx->uID_bits;
char dir[2] = {'+', '-'};
for (k = 0; k < hits->a.n; ++k)
{
fprintf(stderr, "r-%lu-th\t%c\trs-utg%.6dl\t%lu\t%c\tre-utg%.6dl\t%lu\n",
hits->a.a[k].id,
dir[hits->a.a[k].s>>63], (int)((hits->a.a[k].s<<1)>>shif)+1, hits->a.a[k].s&idx->pos_mode,
dir[hits->a.a[k].e>>63], (int)((hits->a.a[k].e<<1)>>shif)+1, hits->a.a[k].e&idx->pos_mode);
}
}
inline void swap_pe_hit_hap(pe_hit_hap* x, pe_hit_hap* y)
{
pe_hit_hap tmp;
tmp = (*x); (*x) = (*y); (*y) = tmp;
}
void dedup_hits(kvec_pe_hit* hits)
void dedup_hits(kvec_pe_hit* hits, uint64_t is_dup)
{
double index_time = yak_realtime();
uint64_t k, l, m = 0, cur;
@@ -2116,20 +2129,23 @@ void dedup_hits(kvec_pe_hit* hits)
if (k == hits->a.n || hits->a.a[k].s != hits->a.a[l].s)
{
if (k - l > 1) radix_sort_pe_hit_an2(hits->a.a + l, hits->a.a + k);
cur = (uint64_t)-1;
while (l < k)
if(is_dup)
{
if(hits->a.a[l].e != cur)
cur = (uint64_t)-1;
while (l < k)
{
cur = hits->a.a[l].e;
hits->a.a[m++] = hits->a.a[l];
if(hits->a.a[l].e != cur)
{
cur = hits->a.a[l].e;
hits->a.a[m++] = hits->a.a[l];
}
l++;
}
l++;
}
l = k;
}
}
hits->a.n = m;
if(is_dup) hits->a.n = m;
fprintf(stderr, "[M::%s::%.3f] ==> Dedup\n", __func__, yak_realtime()-index_time);
}
@@ -14647,7 +14663,7 @@ int alignment_worker_pipeline(sldat_t* sl, const enzyme *fn1, const enzyme *fn2)
}
fprintf(stderr, "[M::%s::%.3f] ==> Qualification\n", __func__, yak_realtime()-index_time);
dedup_hits(&(sl->hits));
dedup_hits(&(sl->hits), 1);
return 1;
}
@@ -16053,6 +16069,15 @@ void tag_reads(ha_ug_index* idx, kvec_pe_hit *u_hits, bubble_type* bub, int8_t *
fprintf(stderr, "[M::%s::] # consistent reads: %lu, # inconsistent reads: %lu\n", __func__, cons, incons);
}
void renew_idx_para(ha_ug_index* idx, ma_ug_t* ug)
{
for (idx->uID_bits=1; (uint64_t)(1<<idx->uID_bits)<(uint64_t)ug->u.n; idx->uID_bits++);
idx->pos_bits = 64 - idx->uID_bits - 1;
idx->uID_mode = (((uint64_t)-1) << (64-idx->uID_bits))>>1;
idx->pos_mode = ((uint64_t)-1) >> (64-idx->pos_bits);
idx->rev_mode = ((uint64_t)1) << 63;
}
int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_opt_t *opt)
{
double index_time = yak_realtime();
@@ -16079,6 +16104,12 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
///debug_hc_hits_v14(&sl.hits, asm_opt.output_file_name, sl.idx);
////dedup_hits(&(sl.hits), sl.idx);
///write_hc_hits_v14(&sl.hits, asm_opt.output_file_name);
sl.hits.uID_bits = idx->uID_bits; sl.hits.pos_mode = idx->pos_mode;
update_switch_unitig(idx->ug, idx->read_g, &(sl.hits), &(idx->t_ch->k_trans), 10, 20, asm_opt.misjoin_len, 0.15);
renew_idx_para(idx, idx->ug);
// print_hits_simp(idx, &sl.hits);
// print_kv_u_trans_t(&(idx->t_ch->k_trans));
hc_links link;