package biocaml

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The OCaml Bioinformatics Library

Install 

dune-project
 Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

  1. S
    Sebastien Mondet
  2. A
    Ashish Agarwal
  3. P
    Philippe Veber
  4. C
    Christophe Troestler
  5. S
    Sergei Lebedev
  6. D
    David Koppstein
  7. A
    Alexander Gryzlov
  8. F
    Francois Berenger

Maintainers

  1. B
    biocaml@googlegroups.com

Sources

v0.10.1.tar.gz
md5=4cf944bcae5d36bf47b67f6bcb2455d7
sha512=0262b5768aefd7c080f664c46c88876fce9a658cc6a87358a77b7112c49ae3042e7ab542e76be5738fbaeda853149b308b48d4897960b5c7ae3b4da71d978bd8

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

Module Biocaml_unix.Bgzf

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

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 : 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 resources 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 seek_in : in_channel -> Core_kernel.Int64.t -> unit

seek_in iz p moves the current handler to the position p, a so-called virtual file offset, as described in paragraph 4.1.1 of the SAM/BAM format specification. The upper 48 bits correspond to a standard file offset which must match a block beginning, and the lower 16 correspond to an offset in the uncompressed data of the block.

val virtual_offset : in_channel -> Core_kernel.Int64.t

virtual_offset iz provides the current position in the file using the same encoding than for seek_in.

exception 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.

    @raise Invalid_arg

    if level is not between 1 and 9.

val of_out_channel : ?level:int -> 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 resources 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.