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for debugging

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chhylp123
2020-10-11 14:32:33 -04:00
parent 7a314d1ef3
commit 89fcb35a64
9 changed files with 192 additions and 41 deletions
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anchor.cpp
+5 -5
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@@ -58,7 +58,7 @@ 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,
kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f_cigar)
kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct)
{
uint32_t i, rlen;
uint64_t k, l;
@@ -73,7 +73,7 @@ kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f
rlen = Get_READ_LENGTH(R_INF, rid); // read length
// get the list of anchors
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);
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, dbg_ct);
// minimizer of queried read
if (ab->mz.m > ab->old_mz_m) {
ab->old_mz_m = ab->mz.m;
@@ -205,14 +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, kvec_t_u64_warp* chain_idx, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, overlap_region* f_cigar)
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, kvec_t_u64_warp* dbg_ct)
{
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, chain_idx, ha_flt_tab, ha_idx, f_cigar);
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, dbg_ct);
if(ha_idx_hp)
{
@@ -242,7 +242,7 @@ int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, kvec_t_u64_warp*
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, chain_idx, ha_flt_tab_hp, ha_idx_hp, f_cigar);
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, dbg_ct);
if(overlap_list->length + overlap_list_hp->length > overlap_list->size)
{