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mempcpy -> memcpy

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chhylp123
2021-09-12 17:43:43 -04:00
parent 5e84db0ec9
commit ab80851b94
9 changed files with 424 additions and 135 deletions
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Assembly.cpp
+10 -6
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@@ -425,6 +425,7 @@ typedef struct {
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;
@@ -441,7 +442,7 @@ typedef struct {
st_mt_t sp;
} ha_ovec_buf_t;
ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov)
ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov, int is_ug)
{
ha_ovec_buf_t *b;
CALLOC(b, 1);
@@ -456,7 +457,8 @@ ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov)
kv_init(b->r_buf.a);
kv_init(b->k_flag.a);
kv_init(b->sp);
b->ab = ha_abuf_init();
if(!is_ug) b->ab = ha_abuf_init();
else b->abl = ha_abufl_init();
if (!b->is_final) {
init_Cigar_record(&b->cigar1);
init_Graph(&b->POA_Graph);
@@ -476,6 +478,7 @@ void ha_ovec_destroy(ha_ovec_buf_t *b)
destory_overlap_region_alloc(&b->olist);
destory_overlap_region_alloc(&b->olist_hp);
ha_abuf_destroy(b->ab);
ha_abufl_destroy(b->abl);
destory_fake_cigar(&(b->tmp_region.f_cigar));
kv_destroy(b->b_buf.a);
kv_destroy(b->r_buf.a);
@@ -526,7 +529,8 @@ int64_t ha_ovec_mem(const ha_ovec_buf_t *b)
mem_olist += r->boundary_cigars.size * sizeof(window_list);
}
mem = ha_abuf_mem(b->ab) + mem_clist + mem_olist;
if(b->ab) mem = ha_abuf_mem(b->ab) + mem_clist + mem_olist;
if(b->abl) mem = ha_abufl_mem(b->abl) + mem_clist + mem_olist;
if (!b->is_final) {
mem += sizeof(Cigar_record) + b->cigar1.lost_base_size + b->cigar1.size * 4;
mem += sizeof(Correct_dumy) + b->correct.size * 8;
@@ -852,7 +856,7 @@ void ha_overlap_and_correct(int round)
// overlap and correct reads
CALLOC(b, asm_opt.thread_num);
for (i = 0; i < asm_opt.thread_num; ++i)
b[i] = ha_ovec_init(0, (round == asm_opt.number_of_round - 1));
b[i] = ha_ovec_init(0, (round == asm_opt.number_of_round - 1),0);
if(ha_idx) hom_cov = asm_opt.hom_cov;
if(ha_idx == NULL) ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, 0, &R_INF, &hom_cov, &het_cov); // build the index
///debug_adapter(&asm_opt, &R_INF);
@@ -1588,7 +1592,7 @@ void ha_overlap_final(void)
CALLOC(b, asm_opt.thread_num);
for (i = 0; i < asm_opt.thread_num; ++i)
b[i] = ha_ovec_init(asm_opt.flag & HA_F_HIGH_HET, 1);///b[i] = ha_ovec_init(1, 1);
b[i] = ha_ovec_init(asm_opt.flag & HA_F_HIGH_HET, 1,0);///b[i] = ha_ovec_init(1, 1);
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, 1, 0, &R_INF, &hom_cov, &het_cov); // build the index
if(asm_opt.flag & HA_F_HIGH_HET)
{
@@ -1644,7 +1648,7 @@ void ug_idx_build(ma_ug_t *ug, int hap_n)
CALLOC(b, asm_opt.thread_num);
for (i = 0; i < asm_opt.thread_num; ++i)
{
b[i] = ha_ovec_init(1, 1);
b[i] = ha_ovec_init(1, 1, 0);
b[i]->ua = &(ug->u);
}