xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-08 05:18:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

expose purge_dups

Browse Source
This commit is contained in:
chhylp123
2020-04-18 00:45:47 -04:00
parent 85c57fd087
commit 7f6725ead3
6 changed files with 117 additions and 36 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Purge_Dups.cpp
+24 -3
View File
@@ -2777,6 +2777,25 @@ ma_ug_t *ug, asg_t *read_g, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex)
}
}
void filter_hap_overlaps_by_length(hap_overlaps_list* all_ovlp, uint32_t minLen)
{
hap_overlaps *x = NULL;
uint32_t v, i, m, uId;
for (v = 0; v < all_ovlp->num; v++)
{
uId = v;
m = 0;
for (i = 0; i < all_ovlp->x[uId].a.n; i++)
{
x = &(all_ovlp->x[uId].a.a[i]);
if(x->x_end_id - x->x_beg_id < minLen) continue;
all_ovlp->x[uId].a.a[m] = (*x);
m++;
}
all_ovlp->x[uId].a.n = m;
}
}
void debug_hap_overlaps(hap_overlaps_list* all_ovlp, hap_overlaps_list* back_all_ovlp)
{
@@ -3569,9 +3588,8 @@ void print_all_purge_ovlp(ma_ug_t *ug, hap_overlaps_list* all_ovlp)
}
void purge_dups(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* reverse_sources,
R_to_U* ruIndex, kvec_asg_arc_t_warp* edge, float density, uint32_t bi_graph_Len, uint32_t long_hap_overlap,
float lable_match_rate, int max_hang, int min_ovlp, long long bubble_dist, float drop_ratio,
uint32_t just_contain)
R_to_U* ruIndex, kvec_asg_arc_t_warp* edge, float density, uint32_t purege_minLen, int max_hang,
int min_ovlp, long long bubble_dist, float drop_ratio, uint32_t just_contain)
{
asg_t *purge_g = NULL;
purge_g = asg_init();
@@ -3651,6 +3669,9 @@ uint32_t just_contain)
// 0.05, &all_ovlp);
// }
filter_hap_overlaps_by_length(&all_ovlp, purege_minLen);
///normalize_hap_overlaps(&all_ovlp, &back_all_ovlp);
normalize_hap_overlaps_advance(&all_ovlp, &back_all_ovlp, ug, read_g, reverse_sources, ruIndex);
///debug_hap_overlaps(&all_ovlp, &back_all_ovlp);