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removed unused ha_sketch

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Heng Li
2020-10-29 11:28:43 -04:00
parent eddb8173da
commit ef8c047559
5 changed files with 43 additions and 141 deletions
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anchor.cpp
+5 -4
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@@ -57,8 +57,8 @@ 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, 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* dbg_ct)
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* dbg_ct)
{
uint32_t i, rlen;
uint64_t k, l;
@@ -205,7 +205,8 @@ 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, kvec_t_u64_warp* dbg_ct)
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;
@@ -302,4 +303,4 @@ int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, kvec_t_u64_warp*
void ha_sort_list_by_anchor(overlap_region_alloc *overlap_list)
{
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}
}