The position of the five prime end of the read.
The position of the five prime end of the read, wrapped as a reference position.
The index into the read sequence.
If the read is not aligned, returns a None. Else, returns a wrapped boolean stating whether this read is a sequence mismatch against the reference at the given offset within the read?
The reference position to check for a mismatch.
Returns true if this read overlaps the given reference position, and the base aligned at this position is a mismatch against the reference genome..
The MdTag if the read is mapped, None otherwise
The reference position to check for overlap.
Returns true if this read overlaps the given reference position.
The quality scores as a list of integers.
The quality scores as a list of integers. Assumes Illumina (33) encoding.
The underlying read.
Parses the text CIGAR representation of the alignment.
On access, parses the attribute tags ("key:type:value" triples) into usable records.
The position of the unclipped end if the read is mapped, None otherwise.
The position of the unclipped end if the read is mapped, None otherwise.
The unclipped position assumes that any clipped bases would've been aligned as an alignment match.
The position of the unclipped start if the read is mapped, None otherwise.
The position of the unclipped start if the read is mapped, None otherwise.
The unclipped position assumes that any clipped bases would've been aligned as an alignment match.
An enriched version of an Avro AlignmentRecord.
The underlying read.