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new ul

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chhylp123
2021-12-11 14:55:36 -05:00
parent b640289b19
commit 9ec286e64e
9 changed files with 470 additions and 27 deletions
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26
Assembly.cpp
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@@ -20,6 +20,7 @@ void ha_sort_list_by_anchor(overlap_region_alloc *overlap_list);
All_reads R_INF;
Debug_reads R_INF_FLAG;
all_ul_t UL_INF;
void get_corrected_read_from_cigar(Cigar_record* cigar, char* pre_read, int pre_length, char* new_read, int* new_length)
{
@@ -417,31 +418,6 @@ long long push_final_overlaps_increment(ma_hit_t_alloc* paf, ma_hit_t_alloc* rev
return available_overlaps;
}
typedef struct {
int is_final, save_ov;
// chaining and overlapping related buffers
UC_Read self_read, ovlp_read;
Candidates_list clist;
overlap_region_alloc olist;
overlap_region_alloc olist_hp;
ha_abuf_t *ab;
ha_abufl_t *abl;
// error correction related buffers
int64_t num_read_base, num_correct_base, num_recorrect_base;
Cigar_record cigar1;
Graph POA_Graph;
Graph DAGCon;
Correct_dumy correct;
haplotype_evdience_alloc hap;
Round2_alignment round2;
kvec_t_u32_warp b_buf;
kvec_t_u64_warp r_buf;
kvec_t_u8_warp k_flag;
overlap_region tmp_region;
ma_utg_v *ua;
st_mt_t sp;
} ha_ovec_buf_t;
ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov, int is_ug)
{
ha_ovec_buf_t *b;