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clean purge_dups

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chhylp123
2021-04-03 16:26:58 -04:00
parent 46e899bbae
commit ebfc04d253
6 changed files with 478 additions and 120 deletions
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Purge_Dups.cpp
+18 -24
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@@ -44,12 +44,6 @@ typedef struct {
uint64_t i;
}kvec_hap_candidates;
#define SELF_EXIST 0
#define REVE_EXIST 1
#define DELETE 2
#define MIXED 3
#define FLIP 4
typedef struct {
uint64_t* vote_counting;
@@ -801,10 +795,7 @@ long long* n_y_beg, long long* n_y_end)
}
#define X2Y 0
#define Y2X 1
#define XCY 2
#define YCX 3
uint32_t classify_hap_overlap(long long xBeg, long long xEnd, long long xLen,
long long yBeg, long long yEnd, long long yLen, long long* r_xBeg, long long* r_xEnd,
long long* r_yBeg, long long* r_yEnd)
@@ -3391,11 +3382,24 @@ double filter_rate)
}
else
{
kv_pushp(hap_overlaps, all_ovlp->x[tn].a, &y);
set_reverse_hap_overlap(y, x, types);
x->status = DELETE;
}
}
}
for (v = 0; v < all_ovlp->num; v++)
{
uId = v;
k = 0;
for (i = 0; i < all_ovlp->x[uId].a.n; i++)
{
if(all_ovlp->x[uId].a.a[i].status == DELETE) continue;
all_ovlp->x[uId].a.a[k] = all_ovlp->x[uId].a.a[i];
k++;
}
all_ovlp->x[uId].a.n = k;
}
}
void filter_hap_overlaps_by_length(hap_overlaps_list* all_ovlp, uint32_t minLen)
@@ -5468,12 +5472,8 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
///if(debug_enable) print_all_purge_ovlp(ug, &all_ovlp);
filter_hap_overlaps_by_length(&all_ovlp, purege_minLen);
if(collect_p_trans)
{
pt_solve(&all_ovlp, cov->t_ch, ug, read_g, 0.8, R_INF.trio_flag);
goto end_coverage;
}
if(asm_opt.polyploidy <= 2) pt_solve(&all_ovlp, cov->t_ch, ug, read_g, 0.8, R_INF.trio_flag);
if(collect_p_trans) goto end_coverage;
pg = init_p_g_t(ug, cov, read_g);
///normalize_hap_overlaps(&all_ovlp, &back_all_ovlp);
@@ -5509,12 +5509,6 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
r = get_hap_arch(&(all_ovlp.x[uId].a.a[i]), ug->u.a[all_ovlp.x[uId].a.a[i].xUid].len,
ug->u.a[all_ovlp.x[uId].a.a[i].yUid].len, max_hang, asm_opt.max_hang_rate, min_ovlp, &t);
// if(all_ovlp.x[uId].a.a[i].xUid == 118 && all_ovlp.x[uId].a.a[i].yUid == 82)
// {
// fprintf(stderr, "r: %d\n", r);
// print_hap_paf(ug, &(all_ovlp.x[uId].a.a[i]));
// }
if(r < 0) continue;
p = asg_arc_pushp(pg->pg_h_lev);
*p = t;