Merge pull request #9 from gofflab/fix/critical-correctness-bugs

Fix critical correctness bugs in complement table and tile overlap

Author: Loyale

VERSIONINFO.md

@@ -1,3 +1,8 @@
+## v0.3.5 - 04.11.2026
+  + Fixed complement table bug: lowercase 'c' was incorrectly complemented to 't' instead of 'g'
+  + Fixed off-by-one in tile overlap detection that caused adjacent non-overlapping tiles to be
+    incorrectly skipped during probe selection, reducing yield
+  + Removed duplicate `__len__` method in Tile class (shadowed definition had off-by-one)
 ## v0.3.4 - 04.10.2026
   + Fixed `designProbes`/`designProbesBatch` reading the species registry from the
     package install directory instead of `~/.hcrprobedesign/HCRconfig.yaml`, which

setup.cfg

@@ -1,7 +1,7 @@
 [metadata]
 # replace with your username:
 name = hcrprobedesign
-version = 0.3.4
+version = 0.3.5
 author = Loyal A. Goff
 author_email = loyalgoff@jhmi.edu
 description = Probe Design tool for Hybridization Chain Reaction

src/HCRProbeDesign/sequencelib.py

@@ -53,7 +53,7 @@ def complement(s):
     :return: A list of the complement bases of the sequence.
     '''
     comp = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N',
-            'a': 't', 'c': 't', 'g': 'c', 't': 'a', 'n': 'n'
+            'a': 't', 'c': 'g', 'g': 'c', 't': 'a', 'n': 'n'
             }
     complseq = [comp[base] for base in s]
     return complseq

src/HCRProbeDesign/tiles.py

@@ -69,13 +69,9 @@ def __iter__(self):
 		"""Iterate over the tile sequence bases."""
 		return iter(self.sequence)
 
-	def __len__(self):
-		"""Return the length of the tile interval."""
-		return self.end-self.start+1
-
 	def overlaps(self,b):
 			"""Return true if b overlaps self"""
-			if (self.start <= b.start and b.start <=self.end) or (self.start >= b.start and self.start <= b.end):
+			if (self.start < b.end and b.start < self.end):
 				return True
 			else:
 				return False

tests/test_sequencelib.py

@@ -0,0 +1,41 @@
+"""Tests for sequencelib complement and reverse_complement functions."""
+
+from HCRProbeDesign import sequencelib
+
+
+def test_complement_uppercase():
+    assert "".join(sequencelib.complement("ACGT")) == "TGCA"
+
+
+def test_complement_lowercase():
+    assert "".join(sequencelib.complement("acgt")) == "tgca"
+
+
+def test_complement_mixed_case():
+    assert "".join(sequencelib.complement("AcGt")) == "TgCa"
+
+
+def test_complement_with_n():
+    assert "".join(sequencelib.complement("ANn")) == "TNn"
+
+
+def test_reverse_complement_uppercase():
+    assert sequencelib.reverse_complement("ACGT") == "ACGT"  # palindrome
+    assert sequencelib.reverse_complement("AACC") == "GGTT"
+
+
+def test_reverse_complement_lowercase():
+    assert sequencelib.reverse_complement("acgt") == "acgt"  # palindrome
+    assert sequencelib.reverse_complement("aacc") == "ggtt"
+
+
+def test_reverse_complement_mixed_case():
+    assert sequencelib.reverse_complement("AaCc") == "gGtT"
+
+
+def test_complement_c_to_g_not_t():
+    """Regression test: lowercase 'c' must complement to 'g', not 't'."""
+    result = "".join(sequencelib.complement("c"))
+    assert result == "g", f"complement('c') returned '{result}', expected 'g'"
+    result = "".join(sequencelib.complement("C"))
+    assert result == "G", f"complement('C') returned '{result}', expected 'G'"

tests/test_tiles.py

@@ -0,0 +1,43 @@
+"""Tests for Tile class overlap detection and __len__."""
+
+from HCRProbeDesign.tiles import Tile
+
+
+def test_len_equals_sequence_length():
+    tile = Tile(sequence="ACGT" * 13, seqName="test", startPos=1)  # 52 bases
+    assert len(tile) == 52
+
+
+def test_overlapping_tiles():
+    t1 = Tile(sequence="A" * 52, seqName="test", startPos=1)
+    t2 = Tile(sequence="A" * 52, seqName="test", startPos=26)  # overlaps with t1
+    assert t1.overlaps(t2)
+    assert t2.overlaps(t1)
+
+
+def test_adjacent_tiles_do_not_overlap():
+    """Regression test: tiles at adjacent non-overlapping positions must not overlap."""
+    t1 = Tile(sequence="A" * 52, seqName="test", startPos=1)   # covers 1..52, end=53
+    t2 = Tile(sequence="A" * 52, seqName="test", startPos=53)  # covers 53..104
+    assert not t1.overlaps(t2), "Adjacent tiles incorrectly flagged as overlapping"
+    assert not t2.overlaps(t1), "Adjacent tiles incorrectly flagged as overlapping"
+
+
+def test_distant_tiles_do_not_overlap():
+    t1 = Tile(sequence="A" * 52, seqName="test", startPos=1)
+    t2 = Tile(sequence="A" * 52, seqName="test", startPos=100)
+    assert not t1.overlaps(t2)
+    assert not t2.overlaps(t1)
+
+
+def test_same_start_overlaps():
+    t1 = Tile(sequence="A" * 52, seqName="test", startPos=10)
+    t2 = Tile(sequence="A" * 52, seqName="test", startPos=10)
+    assert t1.overlaps(t2)
+
+
+def test_one_base_overlap():
+    t1 = Tile(sequence="A" * 52, seqName="test", startPos=1)   # end=53
+    t2 = Tile(sequence="A" * 52, seqName="test", startPos=52)  # starts at 52, within t1
+    assert t1.overlaps(t2)
+    assert t2.overlaps(t1)