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chhylp123
2021-03-14 03:25:19 -04:00
parent 4c2ce6fc6b
commit 8e4b98f0a6
5 changed files with 1161 additions and 406 deletions
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Purge_Dups.cpp
+19 -18
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@@ -2575,11 +2575,12 @@ long long* r_y_pos_beg, long long* r_y_pos_end)
void print_hap_paf(ma_ug_t *ug, hap_overlaps* ovlp)
{
fprintf(stderr, "utg%.6d%c\t%u(%u)\t%u(%u)\t%u(%u)\t%c\tutg%.6d%c\t%u(%u)\t%u(%u)\t%u(%u)\t%u\t%u\n",
fprintf(stderr, "utg%.6d%c\t%u(%u)\t%u(%u)\t%u(%u)\t%c\tutg%.6d%c\t%u(%u)\t%u(%u)\t%u(%u)\t%u\t%u\t%lld(%u)\n",
ovlp->xUid+1, "lc"[ug->u.a[ovlp->xUid].circ], ug->u.a[ovlp->xUid].len, ug->u.a[ovlp->xUid].n,
ovlp->x_beg_pos, ovlp->x_beg_id, ovlp->x_end_pos, ovlp->x_end_id, "+-"[ovlp->rev],
ovlp->yUid+1, "lc"[ug->u.a[ovlp->yUid].circ], ug->u.a[ovlp->yUid].len, ug->u.a[ovlp->yUid].n,
ovlp->y_beg_pos, ovlp->y_beg_id, ovlp->y_end_pos, ovlp->y_end_id, ovlp->type, (uint32_t)ovlp->weight);
ovlp->y_beg_pos, ovlp->y_beg_id, ovlp->y_end_pos, ovlp->y_end_id, ovlp->type, ovlp->weight,
ovlp->score, ovlp->status);
}
inline long long get_max_index(asg_arc_t_offset* x, int32_t* Scores, uint8_t* Flag, long long n,
@@ -3148,6 +3149,7 @@ void set_reverse_hap_overlap(hap_overlaps* dest, hap_overlaps* source, uint32_t*
dest->x_end_id = source->y_end_id;
dest->y_beg_id = source->x_beg_id;
dest->y_end_id = source->x_end_id;
dest->score = source->score;
}
/**
@@ -3409,13 +3411,13 @@ uint64_t asg_bub_pop1_purge_graph(asg_t *g, uint32_t v0, int max_dist, buf_t *b)
///assert(nv > 0);
///all out-edges of v
for (i = 0; i < nv; ++i) { // loop through v's neighbors
///if this edge has been deleted
if (av[i].del) continue;
uint32_t w = av[i].v; // v->w with length l
binfo_t *t = &b->a[w];
///that means there is a circle, directly terminate the whole bubble poping
///if (w == v0) goto pop_reset;
if ((w>>1) == (v0>>1)) goto pop_reset;
///if this edge has been deleted
if (av[i].del) continue;
c_s = decode_score((uint32_t)av[i].ul, av[i].ol);
///push the edge
///high 32-bit of g->idx[v] is the start point of v's edges
@@ -3499,7 +3501,7 @@ pop_reset:
// pop bubbles
int asg_pop_bubble_purge_graph(asg_t *purge_g, int max_dist)
int asg_pop_bubble_purge_graph(asg_t *purge_g)
{
uint32_t v, n_vtx = purge_g->n_seq * 2;
uint64_t n_pop = 0;
@@ -3641,13 +3643,13 @@ int purge_g_arc_del_short_diploid_by_score(asg_t *g, float drop_ratio)
}
void clean_purge_graph(asg_t *purge_g, int max_dist, float drop_ratio)
void clean_purge_graph(asg_t *purge_g, float drop_ratio)
{
uint64_t operation = 1;
while (operation > 0)
{
operation = 0;
operation += asg_pop_bubble_purge_graph(purge_g, max_dist);
operation += asg_pop_bubble_purge_graph(purge_g);
operation += purge_g_arc_del_short_diploid_by_score(purge_g, drop_ratio);
}
@@ -4122,7 +4124,7 @@ hap_cov_t *cov)
}
purge_g->seq[w>>1].c = ALTER_LABLE;
collect_trans_purge_joint_cov(cov, ug, x);
if(cov) collect_trans_purge_joint_cov(cov, ug, x);
// if(buffer.n > 1)
// {
@@ -4263,20 +4265,21 @@ hap_cov_t *cov)
continue;
}
if(cov->link) collect_reverse_unitigs_purge(&b_0, cov->link, ug, all_ovlp);
///if(cov->link) collect_reverse_unitigs_purge(&b_0, cov->link, ug, all_ovlp);
purge_merge(purge_g, ug, all_ovlp, &b_0, ruIndex, reverse_sources, coverage_cut,
read_g, position_index, u_buffer, tailIndex, prevIndex,max_hang, min_ovlp, edge, visit, cov);
}
free(b_0.b.a);
}
void print_all_purge_ovlp(ma_ug_t *ug, hap_overlaps_list* all_ovlp)
void print_all_purge_ovlp(ma_ug_t *ug, hap_overlaps_list* all_ovlp, const char* cmd)
{
fprintf(stderr, "\n%s--->ug->u.n: %u\n", cmd, (uint32_t)ug->u.n);
uint32_t v, uId, i;
for (v = 0; v < all_ovlp->num; v++)
{
uId = v;
if(uId != 96 && uId != 272) continue;
///if(uId != 96 && uId != 272) continue;
for (i = 0; i < all_ovlp->x[uId].a.n; i++)
{
print_hap_paf(ug, &(all_ovlp->x[uId].a.a[i]));
@@ -4571,7 +4574,7 @@ void remove_contained_haplotig(hap_overlaps_list* all_ovlp, ma_ug_t *ug, asg_t*
purge_g->seq[xUid].del = 1;
all_ovlp->x[uId].a.a[i].status = DELETE;
if(cov->link) collect_reverse_unitig_pair(cov->link, ug, &(all_ovlp->x[uId].a.a[i]));
///if(cov->link) collect_reverse_unitig_pair(cov->link, ug, &(all_ovlp->x[uId].a.a[i]));
collect_trans_purge_cov(cov, ug, &(all_ovlp->x[uId].a.a[i]), 0);
}
@@ -4612,8 +4615,8 @@ void remove_contained_haplotig(hap_overlaps_list* all_ovlp, ma_ug_t *ug, asg_t*
void purge_dups(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources,
ma_hit_t_alloc* reverse_sources, 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, uint32_t just_coverage, hap_cov_t *cov)
uint32_t purege_minLen, int max_hang, int min_ovlp, float drop_ratio, uint32_t just_contain,
uint32_t just_coverage, hap_cov_t *cov)
{
asg_t *purge_g = NULL;
purge_g = asg_init();
@@ -4697,17 +4700,15 @@ uint32_t just_contain, uint32_t just_coverage, hap_cov_t *cov)
kt_for(asm_opt.thread_num, hap_alignment_advance_worker, &hap_buf, nsg->n_seq);
///if(debug_enable) print_all_purge_ovlp(ug, &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);
remove_contained_haplotig(&all_ovlp, ug, nsg, purge_g, cov);
if(just_contain == 0)
{
for (v = 0; v < all_ovlp.num; v++)
@@ -4747,7 +4748,7 @@ uint32_t just_contain, uint32_t just_coverage, hap_cov_t *cov)
asg_cleanup(purge_g);
asg_symm(purge_g);
///may need to do transitive reduction
clean_purge_graph(purge_g, bubble_dist, drop_ratio);
clean_purge_graph(purge_g, drop_ratio);
// if(debug_enable) print_purge_gfa(ug, purge_g);
// if(debug_enable) print_all_purge_ovlp(ug, &all_ovlp);