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

v0.10.0.tar.gz

md5=497e3f2f7128a6ca347d66848da38a3d

sha512=4a76ebbafda3bc944afaff40d69791dfe153a0638ef5d7e6e1bc962b7f991d9545cd0af2d7930b39f8b31dbf067d0603cfa03d9b7a49396ab1ae452df47fd1f3

doc/biocaml.unix/Biocaml_unix/Psl/index.html

Module `Biocaml_unix.Psl`

type item = {

matches : int;
(*
number of bases that match that aren't repeats
*)
mismatches : int;
(*
number of bases that don't match
*)
rep_matches : int;
(*
number of bases that match but are part of repeats
*)
n_count : int;
(*
number of 'N' bases
*)
q_num_insert : int;
(*
number of inserts in query
*)
q_base_insert : int;
(*
number of bases inserted in query
*)
t_num_insert : int;
(*
number of inserts in target
*)
t_base_insert : int;
(*
number of bases inserted in target
*)
q_name : string;
(*
query sequence name
*)
q_strand : char;
(*
'+' or '-' for query strand
*)
q_size : int;
(*
query sequence size
*)
q_start : int;
(*
alignment start position in query
*)
q_end : int;
(*
alignment end position in query
*)
t_name : string;
(*
target sequence name
*)
t_strand : char option;
(*
target strand for translated alignments
*)
t_size : int;
(*
target sequence size
*)
t_start : int;
(*
alignment start position in target
*)
t_end : int;
(*
alignment end position in target
*)
block_count : int;
(*
number of blocks in the alignment (a block contains no gaps)
*)
block_sizes : int list;
(*
sizes of each block
*)
q_starts : int list;
(*
starting positions of each block in query
*)
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

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S-Expressions