Decrease too long min. overlap to adapter length

CHANGES.rst

@@ -7,19 +7,21 @@ development version
 
 * Added ``--action=crop`` for removing everything *except* the adapter sequence.
   (The sequence before and after the adapter is removed.) This can be useful if the
-  "adapter" contains wildcards (such as ``N`` nucleotides) that you are interested
-  in.
+  "adapter" contains wildcards (such as ``N``) that you are interested in.
 * :issue:`788`: Added option ``-L`` as a counterpart to ``-l``/``--length``,
   which allows shortening R1 and R2 to different lengths.
-* :issue:`784`: Fix some unexpected trimming results for anchored 5'
+* A too long minimum overlap is now automatically decreased to the length of
+  the adapter. That is, you can use ``-a 'ACGT;o=99'`` to force full-length
+  matches.
+* :issue:`784`: Fixed some unexpected trimming results for anchored 5'
   adapters (due to an incorrectly initialized alignment score matrix).
 
 v4.8 (2024-04-12)
 -------------------
 
-* :issue:`772`: Restore ability to provide input files via
+* :issue:`772`: Restored ability to provide input files via
   process substitution.
-* :issue:`773`: Fix crash when writing interleaved data to stdout
+* :issue:`773`: Fixed crash when writing interleaved data to stdout
   (that is, when no ``-o`` option is provided).
 
 v4.7 (2024-03-14)

src/cutadapt/parser.py

@@ -278,10 +278,7 @@ def parse(cls, spec: str, adapter_type: str) -> "AdapterSpecification":
             )
 
         if parameters.get("min_overlap", 0) > len(spec):
-            raise ValueError(
-                f"min_overlap={parameters['min_overlap']}"
-                f" exceeds length of adapter {spec}"
-            )
+            parameters["min_overlap"] = len(spec)
 
         if rightmost and (adapter_type != "front" or restriction is not None):
             raise ValueError("'rightmost' only allowed with regular 5' adapters")

tests/test_parser.py

@@ -266,9 +266,10 @@ def test_make_adapter_back():
         make_adapter("ACGT$;min_overlap=3", "back", parameters)
     assert "not possible" in e.value.args[0]
 
-    with pytest.raises(ValueError) as e:
-        make_adapter("ACGT;min_overlap=5", "back", parameters)
-    assert "exceeds" in e.value.args[0]
+
+def test_make_adapter_very_long_overlap():
+    a = make_adapter("ACGT;min_overlap=99", "back", {"min_overlap": 1})
+    assert a.min_overlap == 4
 
 
 def test_parse_file_notation_with_parameters(tmp_path):