Representation of partially parsed alignments. When traversing a BAM file for a specific calculation, it may be that only some fields of the alignment records are actually used. In that case, it can be significantly faster to use this representation. As a downside, some encoding errors in the BAM file can go unnoticed.
val qname : t -> string optionval flags : t -> Sam.Flags.t Core.Or_error.tval ref_id : t -> int optionval rname : t -> Header.t -> string option Core.Or_error.tval pos : t -> int optionPositions are 0-based, -1 if undefined
val mapq : t -> int optionval cigar : t -> Sam.cigar_op list Core.Or_error.tval rnext : t -> Header.t -> Sam.rnext option Core.Or_error.tval pnext : t -> int optionval tlen : t -> int optionval seq : t -> string optionval qual : t -> Phred_score.t list Core.Or_error.tval optional_fields : t -> Sam.optional_field list Core.Or_error.tval decode : t -> Header.t -> alignment Core.Or_error.tval encode : alignment -> Header.t -> t Core.Or_error.t