Module Bam.Alignment0Source

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.

Sourcetype t
include Sexplib0.Sexpable.S with type t := t
Sourceval t_of_sexp : Sexplib0.Sexp.t -> t
Sourceval sexp_of_t : t -> Sexplib0.Sexp.t
Sourceval qname : t -> string option
Sourceval ref_id : t -> int option
Sourceval rname : t -> Header.t -> string option Core.Or_error.t
Sourceval pos : t -> int option

Positions are 0-based, -1 if undefined

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