docs: add arg to docstrings

fgpyo/sam/__init__.py

@@ -1196,6 +1196,7 @@ class AuxAlignment(ABC, DataclassInstance):
     Args:
         reference_name: The reference sequence name.
         reference_start: The 0-based start position of the alignment.
+        is_forward: If the alignment is in the forward orientation or not.
         cigar: The Cigar sequence representing the alignment.
         mapq: The aligner-reported probability of an incorrect mapping, if available.
         edit_distance: The number of mismatches between the query and the target, if available.
@@ -1369,13 +1370,15 @@ def many_sam_from_primary(cls, primary: AlignedSegment) -> Iterator[AlignedSegme
             # Finally, set a tag that marks this alignment as a reconstituted auxiliary alignment.
             aux.set_tag("rh", True)
 
-            yield hit.after_sam_from_primary(aux=aux, primary=primary)
+            yield hit._after_sam_from_primary(aux=aux, primary=primary)
 
-    def after_sam_from_primary(
+    def _after_sam_from_primary(
         self, aux: AlignedSegment, primary: AlignedSegment
     ) -> AlignedSegment:
         """Post-processes the reconstituted auxiliary alignment specific to this implementation.
 
+        Override this function to provide implementation-specific behavior.
+
         Args:
             aux: The reconstituted auxiliary alignment.
             primary: The primary alignment that reconstituted the auxiliary alignment.
@@ -1429,6 +1432,7 @@ class SecondaryAlignment(AuxAlignment):
     Args:
         reference_name: The reference sequence name.
         reference_start: The 0-based start position of the alignment.
+        is_forward: If the alignment is in the forward orientation or not.
         cigar: The Cigar sequence representing the alignment.
         mapq: The aligner-reported probability of an incorrect mapping, if available.
         edit_distance: The number of mismatches between the query and the target, if available.
@@ -1487,7 +1491,7 @@ def from_tag_item(cls, item: str) -> Self:
         )
 
     @override
-    def after_sam_from_primary(
+    def _after_sam_from_primary(
         self, aux: AlignedSegment, primary: AlignedSegment
     ) -> AlignedSegment:
         """Post-processes the reconstituted auxiliary alignment as a secondary alignment.
@@ -1499,7 +1503,7 @@ def after_sam_from_primary(
         Raises:
             ValueError: If the primary record is a secondary or supplementary alignment.
         """
-        aux = super().after_sam_from_primary(aux=aux, primary=primary)
+        aux = super()._after_sam_from_primary(aux=aux, primary=primary)
         aux.is_secondary = True
         aux.is_supplementary = False
         aux.is_proper_pair = False
@@ -1525,6 +1529,7 @@ class SupplementaryAlignment(AuxAlignment):
     Args:
         reference_name: The reference sequence name.
         reference_start: The 0-based start position of the alignment.
+        is_forward: If the alignment is in the forward orientation or not.
         cigar: The Cigar sequence representing the alignment.
         mapq: The aligner-reported probability of an incorrect mapping, if available.
         edit_distance: The number of mismatches between the query and the target, if available.
@@ -1571,7 +1576,7 @@ def from_tag_item(cls, item: str) -> Self:
         )
 
     @override
-    def after_sam_from_primary(
+    def _after_sam_from_primary(
         self, aux: AlignedSegment, primary: AlignedSegment
     ) -> AlignedSegment:
         """Post-processes the reconstituted auxiliary alignment as a supplementary alignment.
@@ -1583,7 +1588,7 @@ def after_sam_from_primary(
         Raises:
             ValueError: If the primary record is a secondary or supplementary alignment.
         """
-        aux = super().after_sam_from_primary(aux=aux, primary=primary)
+        aux = super()._after_sam_from_primary(aux=aux, primary=primary)
         aux.is_secondary = False
         aux.is_supplementary = True
         aux.is_proper_pair = primary.is_proper_pair