Module Biocaml_unix.Psl

type item = {
  1. matches : int;
    (*

    number of bases that match that aren't repeats

    *)
  2. mismatches : int;
    (*

    number of bases that don't match

    *)
  3. rep_matches : int;
    (*

    number of bases that match but are part of repeats

    *)
  4. n_count : int;
    (*

    number of 'N' bases

    *)
  5. q_num_insert : int;
    (*

    number of inserts in query

    *)
  6. q_base_insert : int;
    (*

    number of bases inserted in query

    *)
  7. t_num_insert : int;
    (*

    number of inserts in target

    *)
  8. t_base_insert : int;
    (*

    number of bases inserted in target

    *)
  9. q_name : string;
    (*

    query sequence name

    *)
  10. q_strand : char;
    (*

    '+' or '-' for query strand

    *)
  11. q_size : int;
    (*

    query sequence size

    *)
  12. q_start : int;
    (*

    alignment start position in query

    *)
  13. q_end : int;
    (*

    alignment end position in query

    *)
  14. t_name : string;
    (*

    target sequence name

    *)
  15. t_strand : char option;
    (*

    target strand for translated alignments

    *)
  16. t_size : int;
    (*

    target sequence size

    *)
  17. t_start : int;
    (*

    alignment start position in target

    *)
  18. t_end : int;
    (*

    alignment end position in target

    *)
  19. block_count : int;
    (*

    number of blocks in the alignment (a block contains no gaps)

    *)
  20. block_sizes : int list;
    (*

    sizes of each block

    *)
  21. q_starts : int list;
    (*

    starting positions of each block in query

    *)
  22. t_starts : int list;
    (*

    starting positions of each block in target

    *)
}

PSL files. Tested only on PSL files generated by BLAT version 34, which output psLayout version 3 files.

module Error : sig ... end
exception Error of Error.t
val in_channel_to_item_stream : ?buffer_size:int -> ?filename:string -> Core_kernel.In_channel.t -> (item, [> Error.t ]) Core_kernel.result Stream.t
val in_channel_to_item_stream_exn : ?buffer_size:int -> ?filename:string -> Core_kernel.In_channel.t -> item Stream.t
module Transform : sig ... end
val line_to_item : Pos.t -> Line.t -> (item, Error.t) Core_kernel.result

S-Expressions

val item_of_sexp : Sexplib.Sexp.t -> item
val sexp_of_item : item -> Sexplib.Sexp.t