Add properties for whether a variant is an indel, frameshift or SV.

PiperOrigin-RevId: 864449441
Change-Id: I4fc9f6f05dd65f1e5226d99842d684d367fd92ae

Author: tomwardio

src/alphagenome/data/genome.py

@@ -749,6 +749,23 @@ def is_insertion(self) -> bool:
     """Return if the variant is an insertion."""
     return len(self.reference_bases) < len(self.alternate_bases)
 
+  @property
+  def is_frameshift(self) -> bool:
+    """Return if the variant is a frameshift."""
+    indel_size = abs(len(self.reference_bases) - len(self.alternate_bases))
+    return indel_size > 0 and indel_size % 3 != 0
+
+  @property
+  def is_indel(self) -> bool:
+    """Return if the variant is an insertion or deletion."""
+    return self.is_insertion or self.is_deletion
+
+  @property
+  def is_structural(self) -> bool:
+    """Return if the variant is a structural variant."""
+    indel_size = abs(len(self.reference_bases) - len(self.alternate_bases))
+    return indel_size >= 50
+
   def copy(self) -> Self:
     """Returns a deep copy of the variant."""
     return copy.deepcopy(self)

src/alphagenome/data/genome_test.py

@@ -781,6 +781,38 @@ def test_is_insertion(self, ref, alt, expected):
     v = genome.Variant('chr1', 10, ref, alt)
     self.assertEqual(v.is_insertion, expected)
 
+  @parameterized.parameters(
+      ('A', 'C', False),
+      ('AC', 'A', True),
+      ('A', 'AC', True),
+      ('AC', 'GT', False),
+      ('', 'A', True),
+      ('A', '', True),
+  )
+  def test_is_indel(self, ref, alt, expected):
+    v = genome.Variant('chr1', 10, ref, alt)
+    self.assertEqual(v.is_indel, expected)
+
+  @parameterized.parameters(
+      ('A', 'C', False),
+      ('AC', 'GTA', True),
+      ('', 'AAA', False),
+      ('AAAA', 'C', False),
+      ('ACG', 'ACGTACGTN', False),
+  )
+  def test_is_frameshift(self, ref, alt, expected):
+    v = genome.Variant('chr1', 10, ref, alt)
+    self.assertEqual(v.is_frameshift, expected)
+
+  @parameterized.parameters(
+      ('', 'C' * 50, True),
+      ('A' * 51, 'C', True),
+      ('A', 'AC', False),
+  )
+  def test_is_structural(self, ref, alt, expected):
+    v = genome.Variant('chr1', 10, ref, alt)
+    self.assertEqual(v.is_structural, expected)
+
   @parameterized.parameters(
       ('chr1:1:AAA>GGG', 'TTTNNNN', 'chr1:1:AAA>GGG'),
       ('chr1:1:ATCG>ATCC', 'ATCGNNN', 'chr1:4:G>C'),