fix: move bounds check south

prymer/primer3/primer3.py

@@ -373,7 +373,7 @@ def design_primers(self, design_input: Primer3Input) -> Primer3Result:  # noqa:
             )
 
         design_region: Span = self._create_design_region(
-            target=design_input.target,
+            target_region=design_input.target,
             max_amplicon_length=design_input.params.max_amplicon_length,
             min_primer_length=design_input.params.min_primer_length,
         )
@@ -713,7 +713,7 @@ def _build_failures(
 
     def _create_design_region(
         self,
-        target: Span,
+        target_region: Span,
         max_amplicon_length: int,
         min_primer_length: int,
     ) -> Span:
@@ -730,19 +730,22 @@ def _create_design_region(
             ValueError: If the target region is too large to be padded.
 
         """
-        padding: int = max_amplicon_length - target.length
-        contig_length: int = self._dict[target.refname].length
+        padding: int = max_amplicon_length - target_region.length
+        contig_length: int = self._dict[target_region.refname].length
 
-        if padding < min_primer_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
+
+        if left_design_window < min_primer_length or right_design_window < min_primer_length:
             raise ValueError(
-                f"Target region {target} is too large to design an amplicon of maximum "
+                f"Target region {target_region} is too large to design an amplicon of maximum "
                 f"length {max_amplicon_length}."
             )
 
-        design_region: Span = replace(
-            target,
-            start=max(1, target.start - padding),
-            end=min(target.end + padding, contig_length),
-        )
-
         return design_region

tests/primer3/test_primer3.py

@@ -560,24 +560,24 @@ 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:
     """If the target region is shorter than the max amplicon length, it should be padded to fit."""
-    target = Span(refname="chr1", start=201, end=250, strand=Strand.POSITIVE)
+    target_region = Span(refname="chr1", start=201, end=250, strand=Strand.POSITIVE)
 
     with Primer3(genome_fasta=genome_ref) as designer:
         design_region: Span = designer._create_design_region(
-            target=target,
+            target_region=target_region,
             max_amplicon_length=max_amplicon_length,
             min_primer_length=10,
         )
 
-    assert design_region.length == 2 * max_amplicon_length - target.length
+    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."""
-    target = Span(refname="chr1", start=201, end=250, strand=Strand.POSITIVE)
+    target_region = Span(refname="chr1", start=201, end=250, strand=Strand.POSITIVE)
 
     with Primer3(genome_fasta=genome_ref) as designer:
         with pytest.raises(ValueError):
             designer._create_design_region(
-                target=target, max_amplicon_length=10, min_primer_length=10
+                target_region=target_region, max_amplicon_length=10, min_primer_length=10
             )