xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-27 22:38:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

clean purge_dups

Browse Source
This commit is contained in:
chhylp123
2021-04-03 16:26:58 -04:00
parent 46e899bbae
commit ebfc04d253
6 changed files with 478 additions and 120 deletions
Download Patch File Download Diff File Expand all files Collapse all files
partig.cpp
+74
View File
@@ -691,6 +691,78 @@ void set_trio_flag(ma_ug_t *ug, asg_t *read_g, uint32_t uID, uint8_t* trio_flag,
// }
}
void filter_ovlp(ma_ug_t *ug, asg_t *read_g, uint32_t uID, hap_overlaps_list* ha, pt_match_t *ma,
int8_t *s)
{
pt_match1_t *o = pt_a(*ma, uID);
uint32_t n = pt_n(*ma, uID), k, qn, tn;
hap_overlaps *p = NULL;
int index;
for (k = 0; k < n; ++k)
{
qn = o[k].sid[0]; tn = o[k].sid[1]; p = NULL;
if((s[qn]*s[tn])!=-1) continue;
index = get_specific_hap_overlap(&(ha->x[qn]), qn, tn);
if(index != -1 && ha->x[qn].a.a[index].score == (long long)o[k].w)
{
p = &(ha->x[qn].a.a[index]);
}
else
{
index = get_specific_hap_overlap(&(ha->x[tn]), tn, qn);
if(index != -1 && ha->x[tn].a.a[index].score == (long long)o[k].w)
{
p = &(ha->x[tn].a.a[index]);
}
}
if(!p) fprintf(stderr, "ERROR\n");
p->status = FLIP;
}
}
void clean_ovlp(ma_ug_t *ug, asg_t *read_g, hap_overlaps_list* ha, pt_g_t *pg, int8_t* s)
{
uint32_t v, i, k, qn, tn, types[4];
types[X2Y] = Y2X; types[Y2X] = X2Y; types[XCY] = YCX; types[YCX] = XCY;
int index;
hap_overlaps *x = NULL, *y = NULL;
for (i = 0; i < pg->e->n_seq; ++i)
{
filter_ovlp(ug, read_g, i, ha, pg->e, s);
}
for (v = 0; v < ha->num; v++)
{
for (i = 0; i < ha->x[v].a.n; i++)
{
qn = ha->x[v].a.a[i].xUid;
tn = ha->x[v].a.a[i].yUid;
x = &(ha->x[v].a.a[i]);
if(x->status != FLIP) continue;
index = get_specific_hap_overlap(&(ha->x[tn]), tn, qn);
if(index != -1)
{
y = &(ha->x[tn].a.a[index]);
set_reverse_hap_overlap(y, x, types);
y->status = FLIP;
}
if(index == -1) fprintf(stderr, "ERROR\n");
}
}
for (v = 0; v < ha->num; v++)
{
for (i = k = 0; i < ha->x[v].a.n; i++)
{
if(ha->x[v].a.a[i].status != FLIP) continue;
ha->x[v].a.a[k] = ha->x[v].a.a[i];
k++;
}
ha->x[v].a.n = k;
}
}
void pt_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, ma_ug_t *ug, asg_t *read_g, double f_rate, uint8_t* trio_flag)
{
pt_svopt_t opt;
@@ -726,6 +798,8 @@ void pt_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, ma_ug_t *ug, asg_t *re
pg->info.a[i].m[0] = z[0], pg->info.a[i].m[1] = z[1];
}
clean_ovlp(ug, read_g, ovlp, pg, s);
free(buf);
free(s);
destory_pt_g_t(&pg);