Minor fixes to silence warnings and replaced two asprintf uses

src/bloom.c

@@ -61,7 +61,7 @@ static int bloom_check_add(struct bloom * bloom,
   register unsigned int a = murmurhash2(buffer, len, 0x9747b28c);
   register unsigned int b = murmurhash2(buffer, len, a);
   register unsigned int x;
-  register unsigned int i;
+  register int i;	// TODO why was it unsigned?
 
   unsigned bucket_index = (a % bloom->buckets);
 

src/encode.c

@@ -28,9 +28,9 @@
 
 
 
-bool only_ATGC(char* seq)
+bool only_ATGC(const char* seq)
 {
-	char* c = seq;
+	const char* c = seq;
 
 	while (*c)
 	{

src/encode.h

@@ -69,7 +69,7 @@ enum
  * @since November 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-bool only_ATGC(char* seq);
+bool only_ATGC(const char* seq);
 
 
 /**

src/obiavl.c

@@ -483,26 +483,9 @@ int grow_avl(OBIDMS_avl_p avl)		// TODO Lock when needed
 	size_t 	new_data_size;
 	size_t 	header_size;
 	int 	avl_file_descriptor;
-	char* 	avl_file_name;
 
 	avl_file_descriptor = avl->avl_fd;
 
-//	// Get the avl file name
-//	avl_file_name = build_avl_file_name((avl->header)->avl_name);
-//	if (avl_file_name == NULL)
-//		return -1;
-//
-//	// Open the avl file
-//	avl_file_descriptor = openat(avl->dir_fd, avl_file_name, O_RDWR);
-//	if (avl_file_descriptor < 0)
-//	{
-//		obi_set_errno(OBI_AVL_ERROR);
-//		obidebug(1, "\nError opening an AVL tree file");
-//		free(avl_file_name);
-//		return -1;
-//	}
-//	free(avl_file_name);
-
 	// Calculate the new file size
 	old_data_size = (avl->header)->avl_size;
 	new_data_size = old_data_size * AVL_GROWTH_FACTOR;
@@ -563,26 +546,9 @@ int grow_avl_data(OBIDMS_avl_p avl)		// TODO Lock when needed
 	index_t new_data_size;
 	size_t 	header_size;
 	int 	avl_data_file_descriptor;
-	char* 	avl_data_file_name;
 
 	avl_data_file_descriptor = avl->data_fd;
 
-//	// Get the avl data file name
-//	avl_data_file_name = build_avl_data_file_name((avl->header)->avl_name);
-//	if (avl_data_file_name == NULL)
-//		return -1;
-//
-//	// Open the avl data file
-//	avl_data_file_descriptor = openat(avl->dir_fd, avl_data_file_name, O_RDWR);
-//	if (avl_data_file_descriptor < 0)
-//	{
-//		obi_set_errno(OBI_AVL_ERROR);
-//		obidebug(1, "\nError opening an AVL tree data file");
-//		free(avl_data_file_name);
-//		return -1;
-//	}
-//	free(avl_data_file_name);
-
 	// Calculate the new file size
 	old_data_size = ((avl->data)->header)->data_size_max;
 	new_data_size = old_data_size * AVL_GROWTH_FACTOR;
@@ -1014,8 +980,20 @@ OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name)
 	avl_group = (OBIDMS_avl_group_p) malloc(sizeof(OBIDMS_avl_group_t));
 
 	// Create 1st avl
-	asprintf(&avl_name_with_idx,"%s_%u", avl_name, 0);
+	avl_name_with_idx = malloc((strlen(avl_name) + 3)*sizeof(char));
+	if (sprintf(avl_name_with_idx, "%s_%u", avl_name, 0) < 0)
+	{
+		obi_set_errno(OBI_AVL_ERROR);
+		obidebug(1, "\nError building an AVL tree file name");
+		return NULL;
+	}
 	(avl_group->sub_avls)[0] = obi_create_avl(dms, avl_name_with_idx);
+	if ((avl_group->sub_avls)[0] == NULL)
+	{
+		obidebug(1, "\nError creating the first AVL of an AVL group");
+		return NULL;
+	}
+
 	avl_group->current_avl_idx = 0;
 	strcpy(avl_group->avl_name, avl_name);
 
@@ -1039,7 +1017,7 @@ int remap_an_avl(OBIDMS_avl_p avl)
 {
 	(avl->data)->data = mmap(NULL,
 							 ((avl->data)->header)->data_size_max,
-							 PROT_READ | PROT_WRITE,
+							 PROT_READ,
 							 MAP_SHARED,
 							 avl->data_fd,
 							 ((avl->data)->header)->header_size);
@@ -1048,7 +1026,7 @@ int remap_an_avl(OBIDMS_avl_p avl)
 
 	avl->tree = mmap(NULL,
 				((avl->header)->nb_items_max) * sizeof(AVL_node_t),
-				PROT_READ | PROT_WRITE,
+				PROT_READ,
 				MAP_SHARED,
 				avl->avl_fd,
 				(avl->header)->header_size);
@@ -1062,13 +1040,28 @@ int remap_an_avl(OBIDMS_avl_p avl)
 int obi_add_new_avl_in_group(OBIDMS_avl_group_p avl_group)	// TODO check for errors
 {
 	char* avl_name_with_idx;
+	int avl_idx_length;
 
 	// unmap older
 	unmap_an_avl((avl_group->sub_avls)[avl_group->current_avl_idx]);
-
 	(avl_group->current_avl_idx)++;
-	asprintf(&avl_name_with_idx,"%s_%u", avl_group->avl_name, avl_group->current_avl_idx);
+	avl_idx_length = ((avl_group->current_avl_idx) == 0 ? 1 : (int)(log10(avl_group->current_avl_idx)+1));
+	avl_name_with_idx = malloc((strlen(avl_group->avl_name) + avl_idx_length + 2)*sizeof(char));
+	if (sprintf(avl_name_with_idx, "%s_%u", avl_group->avl_name, avl_group->current_avl_idx) < 0)
+	{
+		obi_set_errno(OBI_AVL_ERROR);
+		obidebug(1, "\nError building an AVL tree file name");
+		return -1;
+	}
+
+	//fprintf(stderr, "\nindex length = %d, file name = %s\n", avl_idx_length, avl_name_with_idx);
+
 	(avl_group->sub_avls)[avl_group->current_avl_idx] = obi_create_avl(avl_group->dms, avl_name_with_idx);
+	if ((avl_group->sub_avls)[avl_group->current_avl_idx] == NULL)
+	{
+		obidebug(1, "\nError creating a new AVL tree in a group");
+		return -1;
+	}
 
 	return 0;
 }

src/obiview.c

@@ -228,7 +228,6 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 	if (view== NULL)
 		return NULL;
 
-	fprintf(stderr, "\nmmmm\n");
 	strcpy(view->view_type, VIEW_TYPE_NUC_SEQS);
 
 	if (view_to_clone == NULL)