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Module Biocaml_bgzf (.ml)

I/O on Blocked GNU Zip format (BGZF) files

module Biocaml_bgzf:
sig
type in_channel
Representation of files opened for reading.
val open_in : string -> in_channel
Opens a BGZF file for reading.
Raises Sys_error if the path given in argument does not refer to an existing file.
val of_in_channel : Pervasives.in_channel -> in_channel
Uses a regular channel to read a BGZF compressed file.
val close_in : in_channel -> unit
Closes an open file. The channel cannot be used after that call.
val dispose_in : in_channel -> unit
Releases the ressources associated to a (BGZF) channel (it can thus not be used after that call), apart from the underlying regular channel (which can be used further).
exception Parse_error of string
Exception signaling an incorrect format while reading data from an open file. All input functions may raise this exception.
val input_char : in_channel -> char
val input_u8 : in_channel -> int
val input_s8 : in_channel -> int
val input_u16 : in_channel -> int
val input_s16 : in_channel -> int
val input_s32 : in_channel -> int32
val input : in_channel -> string -> int -> int -> int
input ic buf pos len reads at most len characters in file ic, stores them in string buf at position pos, and returns the number of characters actually read.
val really_input : in_channel -> string -> int -> int -> unit
Same as input but reads exactly len characters.
Raises End_of_file if there are less than len characters available.
val input_string : in_channel -> int -> string
Same as really_input but returns the result in a fresh string.
val with_file_in : string -> f:(in_channel -> 'a) -> 'a
with_file_in fn ~f opens a channel for reading, pass it to f, and returns the result after having closed the channel. If the call to f raises an exception, it is caught and the channel is closed before the exception is re-raised.
type out_channel
Representation of files opened for writing.
val open_out : ?level:int -> string -> out_channel
open_out ~level fn opens the file at path fn for writing a BGZF-compressed file with compression level level (default is 6, legal values are 1 to 9).
Raises
  • Sys_error if fn does not refer to an existing file.
  • Invalid_arg if level is not between 1 and 9.
val of_out_channel : ?level:int -> Pervasives.out_channel -> out_channel
Uses a regular channel to write a BGZF compressed file.
val close_out : out_channel -> unit
Closes a file opened for writing. The channel must not be used after that call.
val dispose_out : out_channel -> unit
Releases the ressources associated to a (BGZF) channel (it can thus not be used after that call), apart from the underlying regular channel (which can be used further).
val output : out_channel -> string -> int -> int -> unit
output oc buf pos len writes len characters of string buf from position pos into the compressed file oc.
val output_char : out_channel -> char -> unit
val output_u8 : out_channel -> int -> unit
output_u8 oz n writes the 8 least significant bits onto channel oz
val output_s8 : out_channel -> int -> unit
output_s8 oz n writes a signed representation of n, if n is between -128 and 127.
Raises Invalid_arg if n is outside this range.
val output_u16 : out_channel -> int -> unit
output_u16 oz n writes the 16 least significant bits onto channel oz
val output_s16 : out_channel -> int -> unit
output_s8 oz n writes a signed representation of n, if n is between -32768 and 32767.
Raises Invalid_arg if n is outside this range.
val output_s32 : out_channel -> int32 -> unit
output_s32 oz n writes a signed representation of n.
val output_string : out_channel -> string -> unit
val with_file_out : ?level:int -> string -> f:(out_channel -> 'a) -> 'a
with_file_out ~level fn ~f opens a file for writing at compression level level (default is 6), passes the channel to f and returns the result after closing the channel. If the call to f raises an exception, it is re-raised after closing the channel.
end