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r185: fixed a few more memory leaks

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This commit is contained in:
Heng Li
2020-04-03 20:14:20 -04:00
parent 6f4d0debe4
commit 992322f8e3
3 changed files with 19 additions and 25 deletions
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Overlaps.cpp
+16 -22
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@@ -4897,12 +4897,10 @@ int asg_arc_del_short_diploid_unclean(asg_t *g, float drop_ratio, ma_hit_t_alloc
uint32_t detect_single_path_with_dels(asg_t *g, uint32_t begNode, uint32_t* endNode, long long* Len, buf_t* b)
{
uint32_t v = begNode, w;
uint32_t kv, kw;
(*Len) = 0;
while (1)
{
(*Len)++;
@@ -5571,6 +5569,7 @@ ma_hit_t_alloc* reverse_sources, long long min_edge_length, R_to_U* ruIndex)
if(flag1 == LOOP || flag2 == LOOP)
{
free(b_0.b.a); free(b_1.b.a);
return -1;
}
@@ -5589,6 +5588,7 @@ ma_hit_t_alloc* reverse_sources, long long min_edge_length, R_to_U* ruIndex)
if(l1 <= min_edge_length || l2 <= min_edge_length)
{
free(b_0.b.a); free(b_1.b.a);
return -1;
}
@@ -13473,22 +13473,22 @@ char* output_file_name)
sprintf(gfa_name, "%s.ovlp", output_file_name);
if(!load_All_reads(&R_INF, gfa_name))
{
free(gfa_name);
return 0;
}
sprintf(gfa_name, "%s.ovlp.source", output_file_name);
if(!load_ma_hit_ts(sources, gfa_name))
{
free(gfa_name);
return 0;
}
sprintf(gfa_name, "%s.ovlp.reverse", output_file_name);
if(!load_ma_hit_ts(reverse_sources, gfa_name))
{
free(gfa_name);
return 0;
}
free(gfa_name);
return 1;
}
@@ -24881,24 +24881,22 @@ int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long n_read, uint64_t* readLen, long long mini_overlap_length,
long long max_hang_length, long long clean_round, long long gap_fuzz,
float min_ovlp_drop_ratio, float max_ovlp_drop_ratio, char* output_file_name,
long long bubble_dist, int read_graph, R_to_U* ruIndex, asg_t* sg,
ma_sub_t* coverage_cut, int debug_g)
long long bubble_dist, int read_graph, R_to_U* ruIndex, asg_t **sg_ptr,
ma_sub_t **coverage_cut_ptr, int debug_g)
{
ma_sub_t *coverage_cut = *coverage_cut_ptr;
asg_t *sg = *sg_ptr;
if(debug_g) goto debug_gfa;
///just for debug
renew_graph_init(sources, reverse_sources, sg, coverage_cut, ruIndex, n_read);
///it's hard to say which function is better
///normalize_ma_hit_t_single_side(sources, n_read);
normalize_ma_hit_t_single_side_advance(sources, n_read);
normalize_ma_hit_t_single_side_advance(reverse_sources, n_read);
// debug_info_of_specfic_read(">m64011_190830_220126/117834372/ccs", sources, reverse_sources,
// -1, "clean");
@@ -25112,13 +25110,13 @@ ma_sub_t* coverage_cut, int debug_g)
bubble_dist, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 0.05, 0.9, max_hang_length,
mini_overlap_length);
output_contig_graph_alternative(sg, coverage_cut, output_file_name, sources, max_hang_length, mini_overlap_length);
}
*coverage_cut_ptr = coverage_cut;
*sg_ptr = sg;
}
void build_string_graph_without_clean(
int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long n_read, uint64_t* readLen, long long mini_overlap_length,
@@ -25131,8 +25129,7 @@ long long bubble_dist, int read_graph, int write)
asg_t *sg = NULL;
ma_sub_t* coverage_cut = NULL;
// debug_info_of_specfic_read("m64011_190329_072846/80545633/ccs",
// sources, reverse_sources, -1, "clean");
// debug_info_of_specfic_read("m64011_190329_072846/80545633/ccs", sources, reverse_sources, -1, "clean");
///actually min_thres = asm_opt.max_short_tip + 1 there are asm_opt.max_short_tip reads
min_thres = asm_opt.max_short_tip + 1;
@@ -25145,7 +25142,7 @@ long long bubble_dist, int read_graph, int write)
clean_graph(min_dp, sources, reverse_sources, n_read, readLen, mini_overlap_length,
max_hang_length, clean_round, gap_fuzz, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
output_file_name, bubble_dist, read_graph, &ruIndex, sg, coverage_cut, 1);
output_file_name, bubble_dist, read_graph, &ruIndex, &sg, &coverage_cut, 1);
asg_destroy(sg);
free(coverage_cut);
destory_R_to_U(&ruIndex);
@@ -25153,20 +25150,17 @@ long long bubble_dist, int read_graph, int write)
}
}
if (asm_opt.write_index_to_disk && write)
{
write_all_data_to_disk(sources, reverse_sources,
&R_INF, output_file_name);
}
try_rescue_overlaps(sources, reverse_sources, n_read, 4);
clean_graph(min_dp, sources, reverse_sources, n_read, readLen, mini_overlap_length,
max_hang_length, clean_round, gap_fuzz, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
output_file_name, bubble_dist, read_graph, &ruIndex, sg, coverage_cut, 0);
output_file_name, bubble_dist, read_graph, &ruIndex, &sg, &coverage_cut, 0);
asg_destroy(sg);
free(coverage_cut);