fixing some checks in options

neat/read_simulator/utils/options.py

@@ -187,7 +187,10 @@ def check_and_log_error(keyname, value_to_check, lowval, highval):
             pass
         elif lowval != "exists" and highval:
             if not (lowval <= value_to_check <= highval):
-                raise ValueError(f'@{keyname} must be between {lowval} and {highval}.\nYour input: {value_to_check}')
+                mssg = f'`{keyname}` must be between {lowval} and {highval} (input: {value_to_check}).'
+                _LOG.error(mssg)
+                raise ValueError(mssg)
+
         elif lowval == "exists" and value_to_check:
             validate_input_path(value_to_check)
 
@@ -204,11 +207,22 @@ def read(self):
                 # if it's already set to the default value, ignore.
                 if value == default or value == ".":
                     continue
-
-                # Now we check that the type is correct and it is in range, depending on the type defined for it
+                # check for empty
+                if value is None:
+                    if key == "reference":
+                        mssg = "Must entered a value for `reference` in config"
+                        _LOG.error(mssg)
+                        raise ValueError(mssg)
+                    else:
+                        _LOG.warning(f"No value entered for `{key}`, skipping.")
+                        continue
+
+                # Now we check that the type is correct, and it is in range, depending on the type defined for it
                 # If it passes that it gets put into the args dictionary.
                 if value != type_of_var(value):
-                    raise ValueError(f"Incorrect type for value entered for {key}: {type_of_var} (found: {value})")
+                    mssg = f"Incorrect type for value entered for {key}: {type_of_var} (found: {value})"
+                    _LOG.error(mssg)
+                    raise ValueError(mssg)
 
                 self.check_and_log_error(key, value, criteria1, criteria2)
                 self.args[key] = value

neat/read_simulator/utils/read.py

@@ -371,7 +371,7 @@ def convert_masking(self, error_model: SequencingErrorModel):
                     modified_segment += base
                 else:
                     modified_segment += repeat_bases[i % 6]
-                    self.num_ns += 1
+                    self.quality_array[i] = bad_score
         else:
             modified_segment = MutableSeq(raw_sequence)