package biotk

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package biotk
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type t = {
  1. total : int;
  2. qc_pass : int;
    (*

    not_passing_quality_controls returns false, assumed for all other counts

    *)
  3. single_reads : int;
    (*

    has_multiple_segments returns false

    *)
  4. read_pairs : int;
    (*

    has_multiple_segments and first_segment

    *)
  5. mapped_reads : int;
    (*

    !segment_unmapped and !secondary_alignment and !supplementary_alignment

    *)
  6. mapped_pairs : int;
    (*

    has_multiple_segments and first_segment and each_segment_properly_aligned and !secondary_alignment and !supplementary_alignment

    *)
}
include Sexplib0.Sexpable.S with type t := t
val t_of_sexp : Sexplib0.Sexp.t -> t
val sexp_of_t : t -> Sexplib0.Sexp.t
val zero : t
val update0 : t -> Bam.Alignment0.t -> t Core.Or_error.t
val update : t -> Sam.alignment -> t
module Fragment_length_histogram : sig ... end
module Chr_histogram : sig ... end
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