Representation of files opened for reading.

Opens a BGZF file for reading.

• raises Sys_error

  if the path given in argument does not refer to an existing file.

Uses a regular channel to read a BGZF compressed file.

Closes an open file. The channel cannot be used after that call.

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).

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.

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

Exception signaling an incorrect format while reading data from an open file. All input functions may raise this exception.

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.

Same as input but reads exactly len characters.

• raises

  End_of_file if there are less than len characters available.

Same as really_input but returns the result in a fresh string.

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.

Representation of files opened for writing.

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.

Uses a regular channel to write a BGZF compressed file.

Closes a file opened for writing. The channel must not be used after that call.

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).

output oc buf ~pos ~len writes len characters of string buf from position pos into the compressed file oc.

Same as output but reading from a string instead of bytes.

output_u8 oz n writes the 8 least significant bits onto channel oz

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.

output_u16 oz n writes the 16 least significant bits onto channel oz

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.

output_s32 oz n writes a signed representation of n.

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.