package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

B

biocaml@googlegroups.com

Sources

v0.11.0.tar.gz

md5=486aeb3e552dabae85839e2af30d6c52

sha512=4ed2df0b7cbd80bd6e29bd8fee9d2dacd9379ad0f4ff142bd8e16ade3f1507f6cc7cbe4c614943b8feb8fa4705935695cb458606b0da813dbf255b1e566a43cf

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_kernel.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_kernel.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