feat: add SAM helpers for isize, set_mate_info, properly_paired

fgpyo/sam/__init__.py

@@ -177,6 +177,7 @@
 from pysam import AlignedSegment
 from pysam import AlignmentFile as SamFile
 from pysam import AlignmentHeader as SamHeader
+from typing_extensions import Self
 from typing_extensions import deprecated
 
 import fgpyo.io
@@ -622,7 +623,7 @@ class PairOrientation(enum.Enum):
     """A pair orientation for tandem (forward-forward or reverse-reverse) pairs."""
 
     @classmethod
-    def build(cls, r1: AlignedSegment, r2: AlignedSegment) -> Self | None:
+    def build(cls, r1: AlignedSegment, r2: AlignedSegment) -> Optional[Self]:
         """Returns the orientation of the read pair if both reads are mapped."""
         if r1.is_unmapped or r2.is_unmapped:
             return None