Merge pull request #455 from chhylp123/hifiasm_dev_debug

fix memory leak of print_utg

Assembly.cpp

@@ -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, 
@@ -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++) 
         {
@@ -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;
 
@@ -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)
 {
@@ -999,8 +1015,7 @@ void ha_overlap_and_correct(int round)
 		ha_ovec_destroy(b[i]);
 	}
 	free(b);
-
+    if (asm_opt.required_read_name) prt_dbg_rs(R_INF_FLAG.fp_r0, &R_INF_FLAG, 0); // for debugging only
-	if (asm_opt.required_read_name) destory_Debug_reads(&R_INF_FLAG), exit(0); // for debugging only
     
 	// save corrected reads to R_INF
 	CALLOC(e, asm_opt.thread_num);
@@ -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();
 }
 

CommandLines.h

@@ -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
 

Overlaps.cpp

@@ -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);

Process_Read.cpp

@@ -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;
@@ -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);
 }
 
@@ -744,8 +755,8 @@ void destory_Debug_reads(Debug_reads* x)
 		kv_destroy(x->candidate_count[i].a);
 	}
 	
-	free(x->read_name);
+	free(x->read_name); free(x->read_id);
-	fclose(x->fp);
+	fclose(x->fp); fclose(x->fp_r0); fclose(x->fp_r1);
 }
 
 

Process_Read.h

@@ -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;