Use a proxy also for --too-long-output

src/cutadapt/cli.py

@@ -92,7 +92,7 @@
     PolyATrimmer,
     PairedReverseComplementer,
 )
-from cutadapt.predicates import TooShort
+from cutadapt.predicates import TooShort, TooLong
 from cutadapt.report import full_report, minimal_report, Statistics
 from cutadapt.pipeline import SingleEndPipeline, PairedEndPipeline
 from cutadapt.runners import make_runner
@@ -475,12 +475,6 @@ def open_output_files(
         ]
     )
 
-    too_long = too_long2 = None
-    if args.maximum_length is not None:
-        too_long, too_long2 = file_opener.xopen_pair(
-            args.too_long_output, args.too_long_paired_output, "wb"
-        )
-
     if (
         int(args.discard_trimmed)
         + int(args.discard_untrimmed)
@@ -549,8 +543,6 @@ def open_output_files(
     return OutputFiles(
         file_opener=file_opener,
         proxied=proxied,
-        too_long=too_long,
-        too_long2=too_long2,
         untrimmed=untrimmed,
         untrimmed2=untrimmed2,
         out=out,
@@ -833,6 +825,12 @@ def make_pipeline_from_args(  # noqa: C901
             args.too_short_paired_output,
             TooShort,
         ),
+        (
+            args.maximum_length,
+            args.too_long_output,
+            args.too_long_paired_output,
+            TooLong,
+        ),
     ]:
         if length is None:
             if path1 or path2:
@@ -841,6 +839,11 @@ def make_pipeline_from_args(  # noqa: C901
                         "When --too-short-output or --too-short-paired-output are used, "
                         "a minimum length must be provided with -m/--minimum-length"
                     )
+                if predicate_class is TooLong:
+                    raise CommandLineError(
+                        "When --too-long-output or --too-long-paired-output are used, "
+                        "a maximum length must be provided with -M/--maximum-length"
+                    )
             continue
         if not paired and path2:
             raise CommandLineError(
@@ -964,18 +967,6 @@ def make_pipeline_from_args(  # noqa: C901
         pipeline.override_untrimmed_pair_filter = True
 
     # Set filtering parameters
-    # Maximum length
-    for attr in ("maximum_length",):
-        param = getattr(args, attr)
-        if param is not None:
-            lengths = parse_lengths(param)
-            if not paired and len(lengths) == 2:
-                raise CommandLineError(
-                    "Two minimum or maximum lengths given for single-end data"
-                )
-            if paired and len(lengths) == 1:
-                lengths = (lengths[0], lengths[0])
-            setattr(pipeline, attr, lengths)
     pipeline.max_n = args.max_n
     pipeline.max_expected_errors = args.max_expected_errors
     pipeline.max_average_error_rate = args.max_average_error_rate

src/cutadapt/files.py

@@ -206,8 +206,6 @@ def __init__(
         out2: Optional[BinaryIO] = None,
         untrimmed: Optional[BinaryIO] = None,
         untrimmed2: Optional[BinaryIO] = None,
-        too_long: Optional[BinaryIO] = None,
-        too_long2: Optional[BinaryIO] = None,
         demultiplex_out: Optional[Dict[str, BinaryIO]] = None,
         demultiplex_out2: Optional[Dict[str, BinaryIO]] = None,
         combinatorial_out: Optional[Dict[Tuple[str, str], BinaryIO]] = None,
@@ -227,8 +225,6 @@ def __init__(
         self.out2 = out2
         self.untrimmed = untrimmed
         self.untrimmed2 = untrimmed2
-        self.too_long = too_long
-        self.too_long2 = too_long2
         self.demultiplex_out = demultiplex_out
         self.demultiplex_out2 = demultiplex_out2
         self.combinatorial_out = combinatorial_out
@@ -287,8 +283,6 @@ def __iter__(self):
             self.out2,
             self.untrimmed,
             self.untrimmed2,
-            self.too_long,
-            self.too_long2,
         ]:
             if f is not None:
                 yield f
@@ -318,8 +312,6 @@ def as_bytesio(self) -> "OutputFiles":
             "out2",
             "untrimmed",
             "untrimmed2",
-            "too_long",
-            "too_long2",
         ):
             if getattr(self, attr) is not None:
                 setattr(result, attr, io.BytesIO())

src/cutadapt/pipeline.py

@@ -25,7 +25,6 @@
 from .predicates import (
     DiscardUntrimmed,
     Predicate,
-    TooLong,
     TooManyN,
     TooManyExpectedErrors,
     TooHighAverageErrorRate,
@@ -65,7 +64,6 @@ def __init__(self) -> None:
         self._textiowrappers: List[TextIO] = []
 
         # Filter settings
-        self._maximum_length = None
         self.max_n = None
         self.max_expected_errors = None
         self.max_average_error_rate = None
@@ -105,21 +103,6 @@ def _set_output(self, outfiles: OutputFiles) -> None:  # noqa: C901
         steps = []
         files: List[Optional[BinaryIO]]
 
-        # minimum length and maximum length
-        for lengths, file1, file2, predicate_class in (
-            (self._maximum_length, outfiles.too_long, outfiles.too_long2, TooLong),
-        ):
-            if lengths is None:
-                continue
-            files = [file1, file2] if self.paired else [file1]
-            writer = self._open_writer(*files) if file1 else None
-            f1 = predicate_class(lengths[0]) if lengths[0] is not None else None
-            if len(lengths) == 2 and lengths[1] is not None:
-                f2 = predicate_class(lengths[1])
-            else:
-                f2 = None
-            steps.append(self._make_filter(predicate1=f1, predicate2=f2, writer=writer))
-
         if self.max_n is not None:
             f1 = f2 = TooManyN(self.max_n)
             steps.append(self._make_filter(f1, f2, None))
@@ -321,15 +304,6 @@ def _create_demultiplexer(self, outfiles: OutputFiles) -> Demultiplexer:
     def _wrap_single_end_step(self, step: SingleEndStep):
         return step
 
-    @property
-    def maximum_length(self):
-        return self._maximum_length
-
-    @maximum_length.setter
-    def maximum_length(self, value):
-        assert value is None or len(value) == 1
-        self._maximum_length = value
-
 
 class PairedEndPipeline(Pipeline):
     """
@@ -471,21 +445,3 @@ def open_writer(file, file2):
 
     def _wrap_single_end_step(self, step: SingleEndStep):
         return PairedSingleEndStep(step)
-
-    @property
-    def minimum_length(self):
-        return self._minimum_length
-
-    @minimum_length.setter
-    def minimum_length(self, value):
-        assert value is None or len(value) == 2
-        self._minimum_length = value
-
-    @property
-    def maximum_length(self):
-        return self._maximum_length
-
-    @maximum_length.setter
-    def maximum_length(self, value):
-        assert value is None or len(value) == 2
-        self._maximum_length = value