Add -q to parallel. This issue is explained in https://stackoverflow.com/questions/8230074/how-to-pass-quoted-args-to-gnu-parallel , which links to : https://www.gnu.org/software/parallel/man.html#QUOTING.

After this fix, #305 should be resolved.

PiperOrigin-RevId: 317875659

Author: pichuan

scripts/run_deepvariant.py

@@ -120,8 +120,16 @@
 }
 
 
+def _is_quoted(value):
+  if value.startswith('"') and value.endswith('"'):
+    return True
+  if value.startswith("'") and value.endswith("'"):
+    return True
+  return False
+
+
 def _add_quotes(value):
-  if isinstance(value, str) and value.startswith('"') and value.endswith('"'):
+  if isinstance(value, str) and _is_quoted(value):
     return value
   return '"{}"'.format(value)
 
@@ -172,7 +180,7 @@ def make_examples_command(ref, reads, examples, extra_args, **kwargs):
   """
   command = [
       'time', 'seq 0 {} |'.format(FLAGS.num_shards - 1),
-      'parallel --halt 2 --line-buffer', '/opt/deepvariant/bin/make_examples'
+      'parallel -q --halt 2 --line-buffer', '/opt/deepvariant/bin/make_examples'
   ]
   command.extend(['--mode', 'calling'])
   command.extend(['--ref', '"{}"'.format(ref)])