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save bfore multiple overlaps

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chhylp123
2020-08-23 08:46:33 -04:00
parent 90d3cb69b9
commit 03cf0d475c
15 changed files with 1120 additions and 131 deletions
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anchor.cpp
+141 -7
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@@ -28,8 +28,8 @@ typedef struct {
} seed1_t;
struct ha_abuf_s {
uint64_t n_a, m_a;
uint32_t old_mz_m;
uint64_t n_a, m_a;///number of anchors (seed positions)
uint32_t old_mz_m;///number of seeds
ha_mz1_v mz;
seed1_t *seed;
anchor1_t *a;
@@ -57,10 +57,9 @@ static int ha_ov_type(const overlap_region *r, uint32_t len)
else return r->x_pos_s == 0? 0 : 1;
}
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain)
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag,
void *ha_flt_tab, ha_pt_t *ha_idx)
{
extern void *ha_flt_tab;
extern ha_pt_t *ha_idx;
uint32_t i, rlen;
uint64_t k, l;
double low_occ = asm_opt.hom_cov * HA_KMER_GOOD_RATIO;
@@ -74,7 +73,8 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
rlen = Get_READ_LENGTH(R_INF, rid); // read length
// get the list of anchors
ha_sketch(ucr->seq, ucr->length, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab);
ha_sketch_query(ucr->seq, ucr->length, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, k_flag);
// minimizer of queried read
if (ab->mz.m > ab->old_mz_m) {
ab->old_mz_m = ab->mz.m;
REALLOC(ab->seed, ab->old_mz_m);
@@ -93,6 +93,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
}
for (i = 0, k = 0; i < ab->mz.n; ++i) {
int j;
///z is one of the minimizer
ha_mz1_t *z = &ab->mz.a[i];
seed1_t *s = &ab->seed[i];
for (j = 0; j < s->n; ++j) {
@@ -116,6 +117,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
}
}
// copy over to _cl_
if (ab->m_a >= (uint64_t)cl->size) {
cl->size = ab->m_a;
@@ -128,6 +130,18 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
p->offset = ab->a[k].other_off;
p->self_offset = ab->a[k].self_off;
p->good = ab->a[k].good;
/***************************************debug**************************************/
if(Get_NAME_LENGTH((R_INF),p->readID)==strlen("m64062_190803_042216/128778853/ccs"))
{
if (memcmp("m64062_190803_042216/128778853/ccs", Get_NAME((R_INF), p->readID),
Get_NAME_LENGTH((R_INF), p->readID)) == 0)
{
fprintf(stderr, "(%lu) readID: %u, strand: %u, offset: %u, self_offset: %u\n",
k, p->readID, p->strand, p->offset, p->self_offset);
}
}
/***************************************debug**************************************/
}
cl->length = ab->n_a;
@@ -172,10 +186,130 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
}
}
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
///ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}
void lable_matched_ovlp(overlap_region_alloc* overlap_list, ma_hit_t_alloc* paf)
{
uint64_t j = 0, inner_j = 0;
while (j < overlap_list->length && inner_j < paf->length)
{
if(overlap_list->list[j].y_id < paf->buffer[inner_j].tn)
{
j++;
}
else if(overlap_list->list[j].y_id > paf->buffer[inner_j].tn)
{
inner_j++;
}
else
{
if(overlap_list->list[j].y_pos_strand == paf->buffer[inner_j].rev)
{
overlap_list->list[j].is_match = 1;
}
j++;
inner_j++;
}
}
}
void ha_get_candidates_interface(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, overlap_region_alloc *overlap_list_hp, Candidates_list *cl, double bw_thres,
int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf)
{
extern void *ha_flt_tab;
extern ha_pt_t *ha_idx;
extern void *ha_flt_tab_hp;
extern ha_pt_t *ha_idx_hp;
ha_get_new_candidates(ab, rid, ucr, overlap_list, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, ha_flt_tab, ha_idx);
if(ha_idx_hp)
{
uint32_t i, k, y_id, overlapLen, max_i;
int shared_seed;
overlap_region t;
overlap_region_sort_y_id(overlap_list->list, overlap_list->length);
ma_hit_sort_tn(paf->buffer, paf->length);
ma_hit_sort_tn(rev_paf->buffer, rev_paf->length);
lable_matched_ovlp(overlap_list, paf);
lable_matched_ovlp(overlap_list, rev_paf);
for (i = 0, k = 0; i < overlap_list->length; ++i)
{
if(overlap_list->list[i].is_match == 1)
{
if(k != i)
{
t = overlap_list->list[k];
overlap_list->list[k] = overlap_list->list[i];
overlap_list->list[i] = t;
overlap_list->list[k].is_match = 0;
}
k++;
}
}
overlap_list->length = k;
ha_get_new_candidates(ab, rid, ucr, overlap_list_hp, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, ha_flt_tab_hp, ha_idx_hp);
if(overlap_list->length + overlap_list_hp->length > overlap_list->size)
{
overlap_list->list = (overlap_region*)realloc(overlap_list->list,
sizeof(overlap_region)*(overlap_list->length + overlap_list_hp->length));
memset(overlap_list->list + overlap_list->size, 0, sizeof(overlap_region)*
(overlap_list->length + overlap_list_hp->length - overlap_list->size));
overlap_list->size = overlap_list->length + overlap_list_hp->length;
}
for (i = 0, k = overlap_list->length; i < overlap_list_hp->length; i++, k++)
{
t = overlap_list->list[k];
overlap_list->list[k] = overlap_list_hp->list[i];
overlap_list_hp->list[i] = t;
}
overlap_list->length = k;
overlap_region_sort_y_id(overlap_list->list, overlap_list->length);
i = k = 0;
while (i < overlap_list->length)
{
y_id = overlap_list->list[i].y_id;
shared_seed = overlap_list->list[i].shared_seed;
overlapLen = overlap_list->list[i].overlapLen;
max_i = i;
i++;
while (i < overlap_list->length && overlap_list->list[i].y_id == y_id)
{
if((overlap_list->list[i].shared_seed > shared_seed) ||
((overlap_list->list[i].shared_seed == shared_seed) && (overlap_list->list[i].overlapLen <= overlapLen)))
{
y_id = overlap_list->list[i].y_id;
shared_seed = overlap_list->list[i].shared_seed;
overlapLen = overlap_list->list[i].overlapLen;
max_i = i;
}
i++;
}
if(k != max_i)
{
t = overlap_list->list[k];
overlap_list->list[k] = overlap_list->list[max_i];
overlap_list->list[max_i] = t;
}
k++;
}
overlap_list->length = k;
}
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}
void ha_sort_list_by_anchor(overlap_region_alloc *overlap_list)
{