package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

github.com Readme Edit opam file Versions (5)

Authors

Maintainers

P

philippe.veber@gmail.com

Sources

biocaml-0.11.2.tbz

sha256=fae219e66db06f81f3fd7d9e44717ccf2d6d85701adb12004ab4ae6d3359dd2d

sha512=f6abd60dac2e02777be81ce3b5acdc0db23b3fa06731f5b2d0b32e6ecc9305fe64f407bbd95a3a9488b14d0a7ac7c41c73a7e18c329a8f18febfc8fd50eccbc6

doc/biocaml.unix/Biocaml_unix/Fastq/Illumina/index.html

Module `Fastq.Illumina`Source

Illumina-specific operations

Sourcetype surface = [

| `Top
| `Bottom

]

Sourcetype tile = private {

surface : surface;
swath : int;
(*
1, 2, or 3
*)
number : int;
(*
1 - 99, but usually 1 - 8
*)

}

Sourceval tile_of_string : string -> tile Core.Or_error.t

E.g. tile_of_string "2304" parses to

surface = Bottom
swath = 3
tile_num = 4

Sourceval tile_to_string : tile -> string

Inverse of tile_of_string.

Sourcetype sequence_id = private {

instrument : string;
run_number : int;
flowcell_id : string;
lane : int;
tile : tile;
x_pos : int;
y_pos : int;
read : int;
is_filtered : bool;
control_number : int;
index : string;

}

Content of name lines as generated by Casava versions >= 1.8.

Sourceval sequence_id_of_string : string -> sequence_id Core.Or_error.t

Parse a name string to a structured Illumina sequence_id. It is assumed that the given string is from an item's name field, i.e. that it doesn't contain a leading @ char.

On This Page

Illumina-specific operations