feat: Add end property on SupplementaryAlignment

Author: msto

fgpyo/sam/__init__.py

@@ -153,6 +153,7 @@
 
 import enum
 import io
+from functools import cached_property
 from pathlib import Path
 from typing import IO
 from typing import Any
@@ -551,6 +552,11 @@ def __str__(self) -> str:
             )
         )
 
+    @cached_property
+    def end(self) -> int:
+        """The 0-based exclusive end position of the alignment."""
+        return self.start + self.cigar.length_on_target()
+
     @staticmethod
     def parse(string: str) -> "SupplementaryAlignment":
         """Returns a supplementary alignment parsed from the given string.  The various fields

fgpyo/sam/tests/test_supplementary_alignments.py

@@ -69,3 +69,12 @@ def test_from_read() -> None:
 
     read = builder.add_single(attrs={"SA": f"{s1};{s2};"})
     assert SupplementaryAlignment.from_read(read) == [sa1, sa2]
+
+
+def test_end() -> None:
+    """Test that we can get the end of a SupplementaryAlignment."""
+
+    s1 = SupplementaryAlignment.parse("chr1,123,+,50S100M,60,0")
+
+    # NB: the SA tag is one-based, but SupplementaryAlignment is zero-based
+    assert s1.end == 222