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Module Biocaml_fastq.Illumina (.ml)

Illumina-specific operations


module Illumina:
sig
type surface = [ `Bottom | `Top ] 
type tile = private {
   surface : surface;
   swath : int; (*1, 2, or 3*)
   number : int; (*1 - 99, but usually 1 - 8*)
} 
val tile_of_string : string -> tile Core.Std.Or_error.t
E.g. tile_of_string "2304" parses to
  • surface = Bottom
  • swath = 3
  • tile_num = 4

val tile_to_string : tile -> string
Inverse of tile_of_string.
type 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.
val sequence_id_of_string : string -> sequence_id Core.Std.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.
end