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fix memory issue

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chhylp123
2024-10-13 18:47:05 -04:00
parent e8b18560a5
commit 49dd83df2a
6 changed files with 235 additions and 33 deletions
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Correct.cpp
+18 -3
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@@ -16753,12 +16753,14 @@ char* qstr, char* tstr, bit_extz_t *exz, double e_rate, int64_t ql, int64_t tl,
uint64_t gen_hc_fast_cigar0(overlap_region *z, Candidates_list *cl, uint64_t wl, All_reads *rref, char* qstr, UC_Read *tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql, uint64_t rid, int64_t h_khit, int64_t *re)
{
int64_t ch_idx = z->shared_seed, ch_n;
int64_t i, tl, id = z->y_id, m, tot_e, aln;
int64_t i, tl, id = z->y_id, m, tot_e, aln, xe, ye;
k_mer_hit *ch_a = cl->list + ch_idx;
tl = Get_READ_LENGTH((*rref), id);
for (i = ch_idx; i < cl->length && cl->list[i].readID == cl->list[ch_idx].readID; i++); ch_n = i-ch_idx;
if(ch_n <= 0) return 0;
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
// fprintf(stderr, "[M::%s::rid->%ld] utg%.6dl(%c), z::[%u, %u)\n",
// __func__, rid, (int32_t)z->y_id+1, "+-"[z->y_pos_strand], z->x_pos_s, z->x_pos_e+1);
@@ -16799,7 +16801,9 @@ uint64_t gen_hc_fast_cigar0(overlap_region *z, Candidates_list *cl, uint64_t wl,
aux_n = z->w_list.n;
for (i = tot_e = aln = 0; i < aux_n; i++) {
if(is_ualn_win(z->w_list.a[i])) {
tot_e += z->w_list.a[i].x_end + 1 - z->w_list.a[i].x_start;
xe = z->w_list.a[i].x_end + 1 - z->w_list.a[i].x_start;
ye = z->w_list.a[i].y_end + 1 - z->w_list.a[i].y_start;
tot_e += ((xe >= ye)?(xe):(ye));
} else {
tot_e += z->w_list.a[i].error; aln += z->w_list.a[i].x_end + 1 - z->w_list.a[i].x_start;
}
@@ -23495,6 +23499,9 @@ void gen_hc_r_alin_nec(overlap_region_alloc* ol, Candidates_list *cl, All_reads
resize_UC_Read(tu, bs<<1);
// fprintf(stderr, "[M::%s] window_length::%lld\n", __func__, w.window_length);
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
for (i = k = 0; i < ol->length; i++) {
z = &(ol->list[i]);
if(z->is_match != 1) {
@@ -23514,11 +23521,19 @@ void gen_hc_r_alin_nec(overlap_region_alloc* ol, Candidates_list *cl, All_reads
if (rr > err) continue;
z->non_homopolymer_errors = re;
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
if(!gen_hc_fast_cigar(z, cl, rref, w.window_length, qu->seq, tu, exz, aux_o, e_rate, ql, rid, khit, &re)) continue;
// if(z->x_id == 3196 && z->y_id == 3199) fprintf(stderr, "-1-[M::%s] tid::%u\t%.*s\trr::%f\tre::%ld\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), rr, re);
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
reassign_gaps(z, aux_o, qu->seq, ql, NULL, -1, rref, tu, buf);
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
}
// if(z->x_id == 3196 && z->y_id == 3199) fprintf(stderr, "-2-[M::%s] tid::%u\t%.*s\trr::%f\tre::%u\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), rr, z->non_homopolymer_errors);