From 02fa015e2850f1b1f7c3b084d7f5ed389886c797 Mon Sep 17 00:00:00 2001
From: chhylp123 <hcheng@jimmy.harvard.edu>
Date: Sat, 13 Feb 2021 23:58:39 -0500
Subject: [PATCH] fix memory leak

---
 Overlaps.cpp |  4 ++--
 hic.cpp      |  9 +++++----
 hifiasm.1    | 15 +++++++++++++++
 3 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/Overlaps.cpp b/Overlaps.cpp
index 3cc16e6..21c8d28 100644
--- a/Overlaps.cpp
+++ b/Overlaps.cpp
@@ -11601,7 +11601,6 @@ void init_hc_links(hc_links* link, uint64_t ug_num, uint64_t r_num)
     {
         kv_init(link->bed.a[i]);
     }
-    
 }
 
 void destory_hc_links(hc_links* link)
@@ -11619,6 +11618,7 @@ void destory_hc_links(hc_links* link)
         kv_destroy(link->bed.a[i]);
     }
     kv_destroy(link->bed);
+    kv_destroy(link->enzymes);
 }
 
 void pop_small_bub(ma_ug_t *ug)
@@ -11855,7 +11855,7 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
     ma_ug_destroy(ug);
     kv_destroy(new_rtg_edges.a);
 
-    ///output_unitig_graph(sg, coverage_cut, output_file_name, sources, ruIndex, max_hang, min_ovlp);
+    output_unitig_graph(sg, coverage_cut, output_file_name, sources, ruIndex, max_hang, min_ovlp);
     output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, 
     reverse_sources, bubble_dist, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 
     0.05, 0.9, max_hang, min_ovlp, 0);
diff --git a/hic.cpp b/hic.cpp
index b235d0d..4e6081d 100644
--- a/hic.cpp
+++ b/hic.cpp
@@ -444,7 +444,7 @@ void hc_pt_t_gen_single(hc_pt1_t* pt, uint64_t* up_bound)
 int write_hc_pt_index(ha_ug_index* idx, char* file_name)
 {
     char* gfa_name = (char*)malloc(strlen(file_name)+25);
-    sprintf(gfa_name, "%s.hc_tlb", file_name);
+    sprintf(gfa_name, "%s.hic.tlb.bin", file_name);
     FILE* fp = fopen(gfa_name, "w");
     if (!fp) {
         free(gfa_name);
@@ -481,7 +481,7 @@ int load_hc_pt_index(ha_ug_index** r_idx, char* file_name)
     uint64_t flag = 0;
     double index_time = yak_realtime();
     char* gfa_name = (char*)malloc(strlen(file_name)+25);
-    sprintf(gfa_name, "%s.hc_tlb", file_name);
+    sprintf(gfa_name, "%s.hic.tlb.bin", file_name);
     FILE* fp = fopen(gfa_name, "r");
     if (!fp) {
         free(gfa_name);
@@ -2142,6 +2142,7 @@ void destory_pdq(pdq* q)
 {
     kv_destroy(q->x);
     kv_destroy(q->dis);
+    kv_destroy(q->vis);
 }
 
 void reset_pdq(pdq* q)
@@ -2889,7 +2890,7 @@ int load_hc_links(hc_links* link, const char *fn)
 void write_hc_hits(kvec_pe_hit* hits, const char *fn)
 {
     char *buf = (char*)calloc(strlen(fn) + 25, 1);
-	sprintf(buf, "%s.hic.lk", fn);
+	sprintf(buf, "%s.hic.lk.bin", fn);
     FILE* fp = fopen(buf, "w");
 
     fwrite(&hits->a.n, sizeof(hits->a.n), 1, fp);
@@ -2903,7 +2904,7 @@ int load_hc_hits(kvec_pe_hit* hits, const char *fn)
 {
     uint64_t flag = 0;
     char *buf = (char*)calloc(strlen(fn) + 25, 1);
-	sprintf(buf, "%s.hic.lk", fn);
+	sprintf(buf, "%s.hic.lk.bin", fn);
 
     FILE* fp = NULL; 
     fp = fopen(buf, "r"); 
diff --git a/hifiasm.1 b/hifiasm.1
index d2e5b36..42bb851 100644
--- a/hifiasm.1
+++ b/hifiasm.1
@@ -384,6 +384,21 @@ phased maternal/haplotype2 contig graph. This graph keeps the phased
 maternal/haplotype2 assembly.
 .RE
 
+.PP
+With Hi-C partition, hifiasm outputs the assembly graphs like trio partition,
+but with additional prefix
+.B [hic].
+In this mode, hifiasm keeps Hi-C alignment results and Hi-C index in two bin 
+files: 
+.B *hic.lk.bin
+and 
+.B *hic.tlb.bin.
+Rerunning hifiasm with different Hi-C reads needs to delete these bin files.
+.RE
+
+
+
+
 .PP
 For each graph, hifiasm also outputs a simplified version without sequences for
 the ease of visualization. Hifiasm keeps corrected reads and overlaps in three