Module Fastq.Illumina

Illumina-specific operations

type surface = [
  1. | `Top
  2. | `Bottom
]
type tile = private {
  1. surface : surface;
  2. swath : int;
    (*

    1, 2, or 3

    *)
  3. number : int;
    (*

    1 - 99, but usually 1 - 8

    *)
}
val 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
val tile_to_string : tile -> string

Inverse of tile_of_string.

type sequence_id = private {
  1. instrument : string;
  2. run_number : int;
  3. flowcell_id : string;
  4. lane : int;
  5. tile : tile;
  6. x_pos : int;
  7. y_pos : int;
  8. read : int;
  9. is_filtered : bool;
  10. control_number : int;
  11. index : string;
}

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

val 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.