refactor: move check south

prymer/primer3/primer3.py

@@ -730,22 +730,33 @@ def _create_design_region(
             ValueError: If the target region is too large to be padded.
 
         """
+        # Pad the target region on both sides by the maximum amplicon length (minus the length of
+        # the target). This ensures that the design region covers the complete window of potentially
+        # valid primer pairs.
         padding: int = max_amplicon_length - target_region.length
-        contig_length: int = self._dict[target_region.refname].length
-
-        design_region: Span = replace(
-            target_region,
-            start=max(1, target_region.start - padding),
-            end=min(target_region.end + padding, contig_length),
-        )
 
-        left_design_window: int = target_region.start - design_region.start
-        right_design_window: int = design_region.end - target_region.end
+        # Apply the padding, ensuring that we don't run out-of-bounds on the target contig.
+        contig_length: int = self._dict[target_region.refname].length
+        design_start: int = max(1, target_region.start - padding)
+        design_end: int = min(target_region.end + padding, contig_length)
 
+        # Validate that our design window includes sufficient space for a primer to be designed on
+        # each side of the target region.
+        left_design_window: int = target_region.start - design_start
+        right_design_window: int = design_end - target_region.end
         if left_design_window < min_primer_length or right_design_window < min_primer_length:
             raise ValueError(
-                f"Target region {target_region} is too large to design an amplicon of maximum "
-                f"length {max_amplicon_length}."
+                f"Target region {target_region} exceeds the maximum size compatible with a "
+                f"maximum amplicon length of {max_amplicon_length} and a minimum primer length of "
+                f"{min_primer_length}. The maximum amplicon length should exceed the length of "
+                "the target region by at least twice the minimum primer length."
             )
 
+        # Return the validated design region.
+        design_region: Span = replace(
+            target_region,
+            start=design_start,
+            end=design_end,
+        )
+
         return design_region

tests/primer3/test_primer3.py

@@ -558,7 +558,7 @@ def test_primer3_result_as_primer_pair_result_exception(
 
 
 @pytest.mark.parametrize("max_amplicon_length", [100, 101])
-def test_pad_target_region(max_amplicon_length: int, genome_ref: Path) -> None:
+def test_create_design_region(max_amplicon_length: int, genome_ref: Path) -> None:
     """If the target region is shorter than the max amplicon length, it should be padded to fit."""
     target_region = Span(refname="chr1", start=201, end=250, strand=Strand.POSITIVE)
 
@@ -572,12 +572,34 @@ def test_pad_target_region(max_amplicon_length: int, genome_ref: Path) -> None:
     assert design_region.length == 2 * max_amplicon_length - target_region.length
 
 
-def test_pad_target_region_doesnt_pad(genome_ref: Path) -> None:
-    """If the target region is larger than the max amplicon length, no padding should occur."""
+def test_create_design_region_raises_when_target_region_exceeds_max_amplicon_length(
+    genome_ref: Path,
+) -> None:
+    """
+    `_create_design_region()` should raise a ValueError when the target region is larger than the
+    max amplicon length.
+    """
     target_region = Span(refname="chr1", start=201, end=250, strand=Strand.POSITIVE)
 
     with Primer3(genome_fasta=genome_ref) as designer:
-        with pytest.raises(ValueError):
+        with pytest.raises(ValueError, match="exceeds the maximum size"):
             designer._create_design_region(
                 target_region=target_region, max_amplicon_length=10, min_primer_length=10
             )
+
+
+def test_create_design_region_raises_when_primers_would_not_fit_in_design_region(
+    genome_ref: Path,
+) -> None:
+    """
+    `_create_design_region()` should raise a ValueError when the design region does not include
+    sufficient space flanking the target for a primer to be designed. (i.e. when this space is less
+    than the specified minimum primer length.)
+    """
+    target_region = Span(refname="chr1", start=201, end=250, strand=Strand.POSITIVE)
+
+    with Primer3(genome_fasta=genome_ref) as designer:
+        with pytest.raises(ValueError, match="exceeds the maximum size"):
+            designer._create_design_region(
+                target_region=target_region, max_amplicon_length=55, min_primer_length=10
+            )