vdjsearch 0.0.5: Fix memory allocation errors

uio-bmi · May 14, 2021 · c568ff3 · c568ff3
1 parent 4ed4730
commit c568ff3
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Showing 5 changed files with 47 additions and 12 deletions.
diff --git a/src/cluster.cc b/src/cluster.cc
@@ -299,7 +299,7 @@ void cluster(char * filename)
   progress_init("Clustering:       ", seqcount);
 
   /* for each non-clustered item, look for subseeds ... */
-
+  uint64_t x = 0;
   for(unsigned int seed = 0; seed < seqcount; seed++)
     {
       struct iteminfo_s * ap = iteminfo + seed;
@@ -315,13 +315,15 @@ void cluster(char * filename)
 
           /* find initial matches */
           process_seed(seed);
+          progress_update(++x);
 
           unsigned int subseed = ap->next;
 
           /* process all subseeds */
           while(subseed != no_cluster)
             {
               process_seed(subseed);
+              progress_update(++x);
               subseed = iteminfo[subseed].next;
             }
 
@@ -339,7 +341,6 @@ void cluster(char * filename)
           sp->size = clustersize;
           clustercount++;
         }
-      progress_update(seed+1);
     }
 
   progress_done();

diff --git a/src/db.cc b/src/db.cc
@@ -98,11 +98,26 @@ void db_init()
 void db_exit()
 {
   if (v_gene_list)
-    xfree(v_gene_list);
-  v_gene_list = 0;
+    {
+      for (uint64_t i = 0; i < v_gene_count; i++)
+	{
+	  xfree(v_gene_list[i]);
+	  v_gene_list[i] = 0;
+	}
+      xfree(v_gene_list);
+      v_gene_list = 0;
+    }
+
   if (j_gene_list)
-    xfree(j_gene_list);
-  j_gene_list = 0;
+    {
+      for (uint64_t i = 0; i < j_gene_count; i++)
+	{
+	  xfree(j_gene_list[i]);
+	  j_gene_list[i] = 0;
+	}
+      xfree(j_gene_list);
+      j_gene_list = 0;
+    }
 }
 
 uint64_t list_insert(char * * * list, uint64_t * alloc, uint64_t * count, char * item)
@@ -382,6 +397,17 @@ void db_hash(struct db * d)
 
 void db_free(struct db * d)
 {
+  if (d->sample_list)
+    {
+      for (uint64_t i = 0; i < d->sample_count; i++)
+	{
+	  xfree(d->sample_list[i]);
+	  d->sample_list[i] = 0;
+	}
+      xfree(d->sample_list);
+      d->sample_list = 0;
+    }
+
   if (d->residues_p)
     xfree(d->residues_p);
   if (d->seqindex)

diff --git a/src/overlap.cc b/src/overlap.cc
@@ -47,7 +47,7 @@ static hashtable_s * hashtable = nullptr;
 
 const uint64_t CHUNK = 1000;
 
-inline void hash_insert(uint64_t amp)
+void hash_insert(uint64_t amp)
 {
   /* set 2 */
   /* find the first empty bucket */
@@ -310,9 +310,13 @@ void overlap(char * set1_filename, char * set2_filename)
 {
   /* find overlaps between repertoires of samples */
 
+  db_init();
+
+
+  /**** Set 1 ****/
+
   fprintf(logfile, "Immune receptor repertoire set 1\n");
 
-  db_init();
   d = db_create();
   db_read(d, set1_filename);
 
@@ -380,6 +384,9 @@ void overlap(char * set1_filename, char * set2_filename)
     fprintf(logfile, "Sum\t%" PRIu64 "\t%7.5lf\n", sum_size, sum_freq);
   fprintf(logfile, "\n");
 
+
+  /**** Set 2 ****/
+
   fprintf(logfile, "Immune receptor repertoire set 2\n");
 
   d2 = db_create();

diff --git a/src/vdjsearch.cc b/src/vdjsearch.cc
@@ -108,7 +108,7 @@ void args_show()
 
 void args_usage()
 {
-  fprintf(stderr, "Usage: %s [OPTIONS] TSVFILE1 [TSVFILE2]\n", PROG_NAME);
+  fprintf(stderr, "Usage: %s [OPTIONS] TSVFILE1 [TSVFILE2]\n", PROG_CMD);
   fprintf(stderr, "\n");
   fprintf(stderr, "Commands:\n");
   fprintf(stderr, " -h, --help                  display this help and exit\n");

diff --git a/src/vdjsearch.h b/src/vdjsearch.h
@@ -95,9 +95,10 @@ static_assert(INT_MAX > 32767, "Your compiler uses very short integers.");
 
 /* constants */
 
-#define PROG_NAME "vdjsearch"
-#define PROG_VERSION "0.0.4"
-#define PROG_BRIEF "Immune repertoire analysis"
+#define PROG_CMD "vdjsearch"
+#define PROG_NAME "VDJsearch"
+#define PROG_VERSION "0.0.5"
+#define PROG_BRIEF "Compare Adaptive Immune Receptor Repertoires"
 
 const unsigned int MAX_THREADS = 256;