Module Bam.Alignment0

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.

type t
include Ppx_sexp_conv_lib.Sexpable.S with type t := t
val t_of_sexp : Sexplib0.Sexp.t -> t
val sexp_of_t : t -> Sexplib0.Sexp.t
val qname : t -> string option
val rname : t -> Header.t -> string option Core_kernel.Or_error.t
val pos : t -> int option

Positions are 0-based, -1 if undefined

val mapq : t -> int option
val rnext : t -> Header.t -> Sam.rnext option Core_kernel.Or_error.t
val pnext : t -> int option
val tlen : t -> int option
val seq : t -> string option
val optional_fields : t -> Sam.optional_field list Core_kernel.Or_error.t