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fix memory leak of print_utg

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chhylp123
2023-05-12 11:31:34 -04:00
parent 18b649aadb
commit 2c18ec30da
5 changed files with 53 additions and 19 deletions
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Overlaps.cpp
+17 -13
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@@ -64,6 +64,8 @@ KRADIX_SORT_INIT(ha_mzl_t_srt1, ha_mzl_t, ha_mzl_t_key, member_size(ha_mzl_t, x)
#define PHASE_SEP_RATE 0.04
#define PHASE_MISS_LEN 1000000
#define PHASE_MISS_N 8
// #define PHASE_MISS_SLEN 500000
// #define PHASE_MISS_SN 24
KSORT_INIT_GENERIC(uint32_t)
@@ -13578,40 +13580,40 @@ void destory_hc_links(hc_links* link)
kv_destroy(link->enzymes);
}
void print_utg(ma_ug_t *ug, asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
void print_utg(ma_ug_t **ug, asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp, kvec_asg_arc_t_warp* new_rtg_edges)
{
if(asm_opt.b_low_cov > 0)
{
break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, new_rtg_edges, max_hang, min_ovlp,
break_ug_contig(ug, sg, &R_INF, coverage_cut, sources, ruIndex, new_rtg_edges, max_hang, min_ovlp,
&asm_opt.b_low_cov, NULL, asm_opt.m_rate);
}
if(asm_opt.b_high_cov > 0)
{
break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, new_rtg_edges, max_hang, min_ovlp,
break_ug_contig(ug, sg, &R_INF, coverage_cut, sources, ruIndex, new_rtg_edges, max_hang, min_ovlp,
NULL, &asm_opt.b_high_cov, asm_opt.m_rate);
}
ma_ug_seq(ug, sg, coverage_cut, sources, new_rtg_edges, max_hang, min_ovlp, 0, 1);
ma_ug_seq(*ug, sg, coverage_cut, sources, new_rtg_edges, max_hang, min_ovlp, 0, 1);
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
sprintf(gfa_name, "%s.p_ctg.gfa", output_file_name);
fprintf(stderr, "Writing %s to disk... \n", gfa_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, sg, coverage_cut, sources, ruIndex, "ptg", output_file);
ma_ug_print(*ug, sg, coverage_cut, sources, ruIndex, "ptg", output_file);
fclose(output_file);
sprintf(gfa_name, "%s.p_ctg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, sg, coverage_cut, sources, ruIndex, "ptg", output_file);
ma_ug_print_simple(*ug, sg, coverage_cut, sources, ruIndex, "ptg", output_file);
fclose(output_file);
if(asm_opt.bed_inconsist_rate != 0)
{
sprintf(gfa_name, "%s.p_ctg.lowQ.bed", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, new_rtg_edges,
ma_ug_print_bed(*ug, sg, &R_INF, coverage_cut, sources, new_rtg_edges,
max_hang, min_ovlp, asm_opt.bed_inconsist_rate, "ptg", output_file, NULL);
fclose(output_file);
}
@@ -15668,7 +15670,7 @@ long long gap_fuzz, bub_label_t* b_mask_t, ug_opt_t *opt)
adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1, 0);
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
print_utg(&copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
if(asm_opt.is_alt)
@@ -15924,7 +15926,7 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, long long gap
adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1, 0);
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
print_utg(&copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
if(asm_opt.is_alt) {
@@ -16920,7 +16922,7 @@ int gap_fuzz, bub_label_t* b_mask_t, ug_opt_t *opt)
// ruIndex, max_hang, min_ovlp, &new_rtg_edges, b_mask_t, NULL);
// exit(1);
/*******************************for debug************************************/
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
print_utg(&copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
@@ -17003,7 +17005,7 @@ long long gap_fuzz, ug_opt_t *opt)
// ruIndex, max_hang, min_ovlp, &new_rtg_edges, b_mask_t, NULL);
// exit(1);
/*******************************for debug************************************/
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
print_utg(&copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
@@ -20546,7 +20548,7 @@ int min_ovlp, int is_bench, long long gap_fuzz, ug_opt_t *opt, bub_label_t* b_ma
reverse_sources, tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate,
drop_ratio, max_hang, min_ovlp, gap_fuzz, 1, b_mask_t, NULL, NULL, &r_edges);
filter_set_kug(R_INF.trio_flag, sg, rf, &r_edges, asm_opt.kpt_rate, &kug);
print_utg(kug, sg, coverage_cut, kug_n, sources, ruIndex, max_hang, min_ovlp, &r_edges);
print_utg(&kug, sg, coverage_cut, kug_n, sources, ruIndex, max_hang, min_ovlp, &r_edges);
free(kug_n), kv_destroy(r_edges.a); ma_ug_destroy(kug);
free(rf);
@@ -20804,7 +20806,9 @@ int min_ovlp, long long gap_fuzz, bub_label_t* b_mask_t, ma_ug_t **rhu0, ma_ug_t
s = dedup_exact_ug(hidx0, hidx1, coverage_cut, sources, ruIndex, ff, MOTHER); dedup_base += s;
destroy_dedup_idx_t(hidx0); destroy_dedup_idx_t(hidx1);
miss_base = append_miss_nid(sg, hu0, hu1, ff, PHASE_MISS_LEN, PHASE_MISS_N); free(ff);
s = append_miss_nid(sg, hu0, hu1, ff, PHASE_MISS_LEN, PHASE_MISS_N); miss_base += s;
// s = append_miss_nid(sg, hu0, hu1, ff, PHASE_MISS_SLEN, PHASE_MISS_SN); miss_base += s;
free(ff);
renew_utg((&hu0), sg, &arcs0); renew_utg((&hu1), sg, &arcs1);
fprintf(stderr, "[M::%s] dedup_base::%lu, miss_base::%lu\n", __func__, dedup_base, miss_base);