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fix scaf bugs

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chhylp123
2024-04-27 07:58:49 -04:00
parent 1ac574adc7
commit 358b090e20
5 changed files with 297 additions and 65 deletions
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horder.cpp
+11 -11
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@@ -714,7 +714,7 @@ void update_u_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, ma_ug_t* ug, asg_t*
kv_pushp(hit_aux_t, x, &p);
p->ruid = u->a[i]>>32;
p->ruid <<= 32;
p->ruid |= v;
p->ruid |= v;///rid|rev|uid
p->off = offset;
offset += (uint32_t)u->a[i];
}
@@ -725,8 +725,8 @@ void update_u_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, ma_ug_t* ug, asg_t*
}
}
radix_sort_hit_aux_ruid(x.a, x.a + x.n);
x.idx.n = x.idx.m = (x.n?(x.a[x.n-1].ruid>>33)+1:0);///how many unitigs
radix_sort_hit_aux_ruid(x.a, x.a + x.n);///sort by (rid|rev|uid)
x.idx.n = x.idx.m = (x.n?(x.a[x.n-1].ruid>>33)+1:0);///how many reads?
CALLOC(x.idx.a, x.idx.n);
for (k = 1, l = 0; k <= x.n; ++k)
{
@@ -2185,7 +2185,7 @@ h_covs *res, h_covs *cov_buf, h_covs *b_points, uint64_t local_bound, int unique
span_e = MIN(span_e, len-1) + 1;
//if(span_e - span_s <= ulen*BREAK_CUTOFF)//need it or not?
{
if(span_s >= sPos && span_e <= ePos)
if(span_s >= sPos && span_e <= ePos)///test the density of this local region; bug -> should use any HiC pairs that are overlapped with [sPos, sPoe), instead of fully covered by [sPos, sPoe)
{
occ++;
if(unique_only && hit->a.a[i].id == 0) continue;
@@ -2590,18 +2590,18 @@ void update_h_w(h_w_t *e, dens_idx_t *idx, double *max_div)
ii = 0;
for (pi = l; pi < k; pi++)
{
pos = e->a[pi].d>>32;///
pos = e->a[pi].d>>32;///loc of 3'-end
while (ii < idn)
{
if(((uint32_t)id[ii]) == pos)
{
if(ori)
if(ori)///the most left one
{
break;
}
else
{
while (ii < idn && (((uint32_t)id[ii]) == pos))
while (ii < idn && (((uint32_t)id[ii]) == pos))///the most right one
{
ii++;
}
@@ -2612,7 +2612,7 @@ void update_h_w(h_w_t *e, dens_idx_t *idx, double *max_div)
ii++;
}
if(ii >= idn) fprintf(stderr, "ERROR-1\n");
e->a[pi].w += (ori? idn-ii: ii+1);
e->a[pi].w += (ori? idn-ii: ii+1);///the smaller the better
if(max_div) (*max_div) = MAX((*max_div), e->a[pi].w);
}
l = k;
@@ -2785,7 +2785,7 @@ void update_scg(horder_t *h, trans_col_t *t_idx)
if(!hits->a.a[i].id) continue;//hom hits
suid = get_hit_suid(*hits, i);
euid = get_hit_euid(*hits, i);
if(suid == euid) continue;
if(suid == euid) continue;//same unitig
slen = ug->u.a[suid].len;
elen = ug->u.a[euid].len;
@@ -2987,7 +2987,7 @@ void get_backbone_layout(horder_t *h, sc_lay_t *sl, osg_t *lg, uint8_t *vis)
{
///I guess this should be (!!(asg_arc_n(lg, k<<1)))^(!!(asg_arc_n(lg, (k<<1)+1)))?
///no, since asg_arc_n is at most 1
if((asg_arc_n(lg, k<<1))^(asg_arc_n(lg, (k<<1)+1)))
if((asg_arc_n(lg, k<<1))^(asg_arc_n(lg, (k<<1)+1)))///end scaffolding
{
v = (asg_arc_n(lg, k<<1)?(k<<1):((k<<1)+1));
if(vis[k<<1] || vis[(k<<1)+1]) continue;
@@ -3512,7 +3512,7 @@ void generate_scaffold(ma_utg_t *su, lay_t *ly, ma_ug_t *pug, asg_t *rg)
}
if(i < ly->n - 2) kv_push(uint64_t, *su, (uint64_t)-1);
}
if(ly->n != 2) is_circle = 0;
if(ly->n != 2) is_circle = 0;///ly-> == 2: single circle
for (i = 0, totalLen = 0; i < su->n-1; i++)
{