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Module Biocaml_bam_alt.Alignment0 (.ml)

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.

module Alignment0:
sig
type t 
val qname : t -> string option
val flags : t -> Biocaml_sam.Flags.t Core.Std.Or_error.t
val rname : t ->
       Biocaml_bam_alt.Header.t -> string option Core.Std.Or_error.t
val pos : t -> int option
val mapq : t -> int option
val cigar : t -> Biocaml_sam.cigar_op list Core.Std.Or_error.t
val rnext : t ->
       Biocaml_bam_alt.Header.t -> Biocaml_sam.rnext option Core.Std.Or_error.t
val pnext : t -> int option
val tlen : t -> int option
val seq : t -> string option
val qual : t ->
       Biocaml_phred_score.t list Core.Std.Or_error.t
val optional_fields : t ->
       Biocaml_sam.optional_field list Core.Std.Or_error.t
val decode : t ->
       Biocaml_bam_alt.Header.t -> Biocaml_bam_alt.alignment Core.Std.Or_error.t
val encode : Biocaml_bam_alt.alignment ->
       Biocaml_bam_alt.Header.t -> t Core.Std.Or_error.t
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
end