package biocaml

  1. Overview
  2. Docs
The OCaml Bioinformatics Library

Install 

dune-project
 Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

  1. S
    Sebastien Mondet
  2. A
    Ashish Agarwal
  3. P
    Philippe Veber
  4. C
    Christophe Troestler
  5. S
    Sergei Lebedev
  6. D
    David Koppstein
  7. A
    Alexander Gryzlov
  8. F
    Francois Berenger

Maintainers

  1. B
    biocaml@googlegroups.com

Sources

v0.10.0.tar.gz
md5=497e3f2f7128a6ca347d66848da38a3d
sha512=4a76ebbafda3bc944afaff40d69791dfe153a0638ef5d7e6e1bc962b7f991d9545cd0af2d7930b39f8b31dbf067d0603cfa03d9b7a49396ab1ae452df47fd1f3

doc/biocaml.ez/Biocaml_ez/Bamstats/index.html

Module Biocaml_ez.Bamstats

include module type of struct include Biocaml_unix.Bamstats end
type t = Biocaml_unix.Bamstats.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 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 zero : t
val update0 : t -> Biocaml_unix.Bam.Alignment0.t -> t Core_kernel.Or_error.t
val update : t -> Biocaml_unix.Sam.alignment -> t
module Fragment_length_histogram = Biocaml_unix.Bamstats.Fragment_length_histogram