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freeze-r304

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chhylp123
2020-08-23 23:34:36 -04:00
parent 03cf0d475c
commit 724990cbe7
7 changed files with 235 additions and 74 deletions
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anchor.cpp
+6 -18
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@@ -50,7 +50,7 @@ uint64_t ha_abuf_mem(const ha_abuf_t *ab)
return ab->m_a * sizeof(anchor1_t) + ab->mz.m * (sizeof(ha_mz1_t) + sizeof(seed1_t)) + sizeof(ha_abuf_t);
}
static int ha_ov_type(const overlap_region *r, uint32_t len)
int ha_ov_type(const overlap_region *r, uint32_t len)
{
if (r->x_pos_s == 0 && r->x_pos_e == len - 1) return 2; // contained in a longer read
else if (r->x_pos_s > 0 && r->x_pos_e < len - 1) return 3; // containing a shorter read
@@ -58,7 +58,7 @@ static int ha_ov_type(const overlap_region *r, uint32_t len)
}
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)
kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f_cigar)
{
uint32_t i, rlen;
uint64_t k, l;
@@ -130,22 +130,10 @@ void *ha_flt_tab, ha_pt_t *ha_idx)
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;
calculate_overlap_region_by_chaining(cl, overlap_list, rid, ucr->length, &R_INF, bw_thres, keep_whole_chain);
calculate_overlap_region_by_chaining(cl, overlap_list, chain_idx, rid, ucr->length, &R_INF, bw_thres, keep_whole_chain, f_cigar);
#if 0
if (overlap_list->length > 0) {
@@ -217,14 +205,14 @@ void lable_matched_ovlp(overlap_region_alloc* overlap_list, ma_hit_t_alloc* paf)
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)
int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* chain_idx, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, overlap_region* f_cigar)
{
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);
ha_get_new_candidates(ab, rid, ucr, overlap_list, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, chain_idx, ha_flt_tab, ha_idx, f_cigar);
if(ha_idx_hp)
{
@@ -254,7 +242,7 @@ int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, ma_hit_t_alloc* p
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);
ha_get_new_candidates(ab, rid, ucr, overlap_list_hp, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, chain_idx, ha_flt_tab_hp, ha_idx_hp, f_cigar);
if(overlap_list->length + overlap_list_hp->length > overlap_list->size)
{