Utils: new function to copy the content of a file into another file

src/utils.c

@@ -36,6 +36,66 @@
  **********************************************************************/
 
 
+int copy_file(const char* src_file_path, const char* dest_file_path)
+{
+	int src_fd, dst_fd, n, err;
+	unsigned char buffer[4096];
+
+	src_fd = open(src_file_path, O_RDONLY);
+	if (src_fd == -1)
+    {
+		obi_set_errno(OBI_UTILS_ERROR);
+		obidebug(1, "\nError opening a file to copy");
+        return -1;
+    }
+    dst_fd = open(dest_file_path, O_CREAT | O_WRONLY, 0777);  // overwrite if already exists
+    if (dst_fd == -1)
+    {
+		obi_set_errno(OBI_UTILS_ERROR);
+		obidebug(1, "\nError opening a file to write a copy: %s", dest_file_path);
+        return -1;
+    }
+
+    while (1)
+    {
+        err = read(src_fd, buffer, 4096);
+        if (err == -1)
+        {
+    		obi_set_errno(OBI_UTILS_ERROR);
+    		obidebug(1, "\nProblem reading a file to copy");
+            return -1;
+        }
+        n = err;
+
+        if (n == 0)
+        	break;
+
+        err = write(dst_fd, buffer, n);
+        if (err == -1)
+        {
+    		obi_set_errno(OBI_UTILS_ERROR);
+    		obidebug(1, "\nProblem writing to a file while copying");
+            return -1;
+        }
+    }
+
+    if (close(src_fd) < 0)
+    {
+		obi_set_errno(OBI_UTILS_ERROR);
+		obidebug(1, "\nError closing a file after copying it");
+        return -1;
+    }
+    if (close(dst_fd) < 0)
+    {
+		obi_set_errno(OBI_UTILS_ERROR);
+		obidebug(1, "\nError closing a file after copying to it");
+        return -1;
+    }
+
+    return 0;
+}
+
+
 int digit_count(index_t i)
 {
 	int n_digits;

src/utils.h

@@ -25,6 +25,20 @@
 #define ONE_IF_ZERO(x) (((x)==0)?1:(x))	/**< If x is equal to 0, x takes the value 1.
                                 	   	 */
 
+/**
+ * @brief Copy the content of a file into another file.
+ *
+ * @param src_file_path The path to the source file to copy.
+ * @param dest_file_path The path to the destination file.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since July 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int copy_file(const char* src_file_path, const char* dest_file_path);
+
 
 /**
  * @brief Counts the number of digits of a number.