diff --git a/pysam/libcalignedsegment.pyi b/pysam/libcalignedsegment.pyi index 4e4b1d6b..bea806e7 100644 --- a/pysam/libcalignedsegment.pyi +++ b/pysam/libcalignedsegment.pyi @@ -88,8 +88,12 @@ class AlignedSegment: is_proper_pair: bool is_unmapped: bool mate_is_unmapped: bool + is_mapped: bool + mate_is_mapped: bool is_reverse: bool mate_is_reverse: bool + is_forward: bool + mate_is_forward: bool is_read1: bool is_read2: bool is_secondary: bool @@ -121,6 +125,10 @@ class AlignedSegment: @property def query_alignment_end(self) -> int: ... @property + def modified_bases(self) -> Optional[Dict[Tuple[str, int, str], List[Tuple[int, int]]]]: ... + @property + def modified_bases_forward(self) -> Optional[Dict[Tuple[str, int, str], List[Tuple[int, int]]]]: ... + @property def query_alignment_length(self) -> int: ... def infer_query_length(self) -> Optional[int]: ... def infer_read_length(self) -> Optional[int]: ...