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fix memory leak of print_utg #455

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May 12, 2023
Merged

fix memory leak of print_utg #455

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22 changes: 20 additions & 2 deletions Assembly.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -700,6 +700,7 @@ static void worker_ovec_related_reads(void *data, long i, int tid)

if(k < R_INF_FLAG.query_num)
{
R_INF_FLAG.read_id[k] = i;
int fully_cov, abnormal, q_idx = k;

ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist,
Expand Down Expand Up @@ -766,6 +767,7 @@ static void worker_ovec_related_reads(void *data, long i, int tid)
Get_READ_LENGTH(R_INF, b->olist.list[k].y_id));
}

/**
fprintf(R_INF_FLAG.fp, "***************************unmatched ovlp***************************\n");
for (k = 0; k < b->olist.length; k++)
{
Expand All @@ -777,6 +779,7 @@ static void worker_ovec_related_reads(void *data, long i, int tid)
b->olist.list[k].y_pos_strand, b->olist.list[k].strong, b->olist.list[k].without_large_indel,
Get_READ_LENGTH(R_INF, b->olist.list[k].y_id));
}
**/

R_INF.trio_flag[i] = AMBIGU;

Expand Down Expand Up @@ -950,6 +953,19 @@ void print_het_cnt_log(uint32_t *het_cnt)
fclose(output_file);
}

void prt_dbg_rs(FILE *fp, Debug_reads* x, uint64_t round)
{
uint64_t k, id; UC_Read g_read; init_UC_Read(&g_read);
for (k = 0; k < R_INF_FLAG.query_num; k++) {
id = x->read_id[k];
if(id == ((uint64_t)-1)) continue;
recover_UC_Read(&g_read, &R_INF, id);
fprintf(fp, ">%.*s_r%lu\n", (int)Get_NAME_LENGTH((R_INF), id), Get_NAME((R_INF), id), round);
fprintf(fp, "%.*s\n", (int)g_read.length, g_read.seq);
}
destory_UC_Read(&g_read);
}


void ha_overlap_and_correct(int round)
{
Expand Down Expand Up @@ -999,8 +1015,7 @@ void ha_overlap_and_correct(int round)
ha_ovec_destroy(b[i]);
}
free(b);

if (asm_opt.required_read_name) destory_Debug_reads(&R_INF_FLAG), exit(0); // for debugging only
if (asm_opt.required_read_name) prt_dbg_rs(R_INF_FLAG.fp_r0, &R_INF_FLAG, 0); // for debugging only

// save corrected reads to R_INF
CALLOC(e, asm_opt.thread_num);
Expand All @@ -1017,6 +1032,9 @@ void ha_overlap_and_correct(int round)
free(e[i].second_round_read);
}
free(e);

if (asm_opt.required_read_name) prt_dbg_rs(R_INF_FLAG.fp_r1, &R_INF_FLAG, 1); // for debugging only
if (asm_opt.required_read_name) destory_Debug_reads(&R_INF_FLAG), exit(0); // for debugging only
///debug_print_pob_regions();
}

Expand Down
2 changes: 1 addition & 1 deletion CommandLines.h
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
#include <pthread.h>
#include <stdint.h>

#define HA_VERSION "0.19.5-r587"
#define HA_VERSION "0.19.5-r589"

#define VERBOSE 0

Expand Down
30 changes: 17 additions & 13 deletions Overlaps.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand Down Expand Up @@ -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);
}
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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) {
Expand Down Expand Up @@ -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);
Expand Down Expand Up @@ -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);
Expand Down Expand Up @@ -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);
Expand Down Expand Up @@ -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);
Expand Down
15 changes: 13 additions & 2 deletions Process_Read.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -714,6 +714,8 @@ void init_Debug_reads(Debug_reads* x, const char* file)
}
x->read_name = (char**)malloc(sizeof(char*)*x->query_num);
x->candidate_count = (kvec_t_u64_warp*)malloc(sizeof(kvec_t_u64_warp)*x->query_num);
x->read_id = NULL; MALLOC(x->read_id, x->query_num);
memset(x->read_id, -1, sizeof((*(x->read_id)))*x->query_num);
fseek(x->fp, 0, SEEK_SET);

i = 0;
Expand All @@ -732,6 +734,15 @@ void init_Debug_reads(Debug_reads* x, const char* file)
sprintf(Name_Buffer, "%s.debug.stdout", file);
x->fp = fopen(Name_Buffer,"w");
fprintf(stderr, "Print debugging information to: %s\n", Name_Buffer);

sprintf(Name_Buffer, "%s.debug.r0.fa", file);
x->fp_r0 = fopen(Name_Buffer,"w");
fprintf(stderr, "Print raw reads to: %s\n", Name_Buffer);

sprintf(Name_Buffer, "%s.debug.r1.fa", file);
x->fp_r1 = fopen(Name_Buffer,"w");
fprintf(stderr, "Print corrected reads to: %s\n", Name_Buffer);

free(Name_Buffer);
}

Expand All @@ -744,8 +755,8 @@ void destory_Debug_reads(Debug_reads* x)
kv_destroy(x->candidate_count[i].a);
}

free(x->read_name);
fclose(x->fp);
free(x->read_name); free(x->read_id);
fclose(x->fp); fclose(x->fp_r0); fclose(x->fp_r1);
}


Expand Down
3 changes: 2 additions & 1 deletion Process_Read.h
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Expand Up @@ -151,9 +151,10 @@ typedef struct
typedef struct
{
char** read_name;
uint64_t *read_id;
uint64_t query_num;
kvec_t_u64_warp* candidate_count;
FILE* fp;
FILE *fp, *fp_r0, *fp_r1;
pthread_mutex_t OutputMutex;
} Debug_reads;

Expand Down