diff --git a/fsverity/fsverity_manifest_generator.py b/fsverity/fsverity_manifest_generator.py
index 99e66c6..1a2fba2 100644
--- a/fsverity/fsverity_manifest_generator.py
+++ b/fsverity/fsverity_manifest_generator.py
@@ -31,7 +31,7 @@
   cmd = [fsverity_path, 'digest', input_file]
   cmd.extend(['--compact'])
   cmd.extend(['--hash-alg', HASH_ALGORITHM])
-  out = subprocess.check_output(cmd, universal_newlines=True).strip()
+  out = subprocess.check_output(cmd, text=True).strip()
   return bytes(bytearray.fromhex(out))
 
 if __name__ == '__main__':
@@ -46,19 +46,28 @@
       required=True)
   p.add_argument(
       '--base-dir',
-      help='directory to use as a relative root for the inputs',
-      required=True)
+      help='directory to use as a relative root for the inputs. Also see the documentation of '
+      'inputs')
   p.add_argument(
       'inputs',
       nargs='*',
-      help='input file for the build manifest')
+      help='input file for the build manifest. It can be in either of two forms: <file> or '
+      '<file>,<path_on_device>. If the first form is used, --base-dir must be provided, and the '
+      'path on device will be the filepath relative to the base dir')
   args = p.parse_args()
 
   links = {}
   digests = FSVerityDigests()
   for f in sorted(args.inputs):
-    # f is a full path for now; make it relative so it starts with {mount_point}/
-    rel = os.path.relpath(f, args.base_dir)
+    if args.base_dir:
+      # f is a full path for now; make it relative so it starts with {mount_point}/
+      rel = os.path.relpath(f, args.base_dir)
+    else:
+      parts = f.split(',')
+      if len(parts) != 2 or not parts[0] or not parts[1]:
+        sys.exit("Since --base-path wasn't provided, all inputs must be pairs separated by commas "
+          "but this input wasn't: " + f)
+      f, rel = parts
 
     # Some fsv_meta files are links to other ones. Don't read through the link, because the
     # layout of files in the build system may not match the layout of files on the device.