package biocaml
The OCaml Bioinformatics Library
Install
Dune Dependency
Authors
Maintainers
Sources
biocaml-0.11.2.tbz
sha256=fae219e66db06f81f3fd7d9e44717ccf2d6d85701adb12004ab4ae6d3359dd2d
sha512=f6abd60dac2e02777be81ce3b5acdc0db23b3fa06731f5b2d0b32e6ecc9305fe64f407bbd95a3a9488b14d0a7ac7c41c73a7e18c329a8f18febfc8fd50eccbc6
doc/src/biocaml.unix/zip.ml.html
Source file zip.ml
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open CFStream module Default = struct let zlib_buffer_size = 4096 let level = 3 end module Error = struct type unzip = [ `garbage_at_end_of_compressed_data of string | `zlib of string | `wrong_gzip_header of [ `compression_method | `flags | `magic_number ] * int ] [@@deriving sexp] (** The possible unzipping errors. *) type t = unzip [@@deriving sexp] end module Transform = struct let try_skip_gzip_header_exn buffer = let open Result.Monad_infix in let bytes_read = ref 0 in let ignore_bytes n = bytes_read := !bytes_read + n in let assert_byte f error = let byte = (Char.to_int (Bytes.get buffer (!bytes_read))) in if f byte then (incr bytes_read; Ok byte) else Error (`wrong_gzip_header (error, byte)) in let assert_byte_eq b error = assert_byte ((=) b) error in let read_byte () = let byte = (Char.to_int (Bytes.get buffer (!bytes_read))) in (incr bytes_read; Ok byte) in let rec skip_null_terminated () = read_byte () >>= fun x -> if x = 0 then Ok () else skip_null_terminated () in assert_byte_eq 0x1f `magic_number >>= fun _ -> assert_byte_eq 0x8b `magic_number >>= fun _ -> assert_byte_eq 8 `compression_method >>= fun _ -> assert_byte (fun b -> b land 0xe0 = 0) `flags >>= fun flags -> ignore_bytes 6; (if flags land 0x04 <> 0 then ( (* Skip extra data *) read_byte () >>= fun len1 -> read_byte () >>= fun len2 -> ignore_bytes (len1 + len2 lsl 8); Ok () ) else Ok ()) >>= fun () -> (if flags land 0x08 <> 0 then skip_null_terminated () else Ok ()) >>= fun () -> (if flags land 0x10 <> 0 then skip_null_terminated () else Ok ()) >>= fun () -> if flags land 0x02 <> 0 then begin (* Skip header CRC *) ignore_bytes 2; end; if !bytes_read > Bytes.length buffer then failwith "NOT-YET" else Ok !bytes_read let inflate_as_much_as_possible in_buffer buffer zstream zlib_write_buffer zlib_buffer_size format = let len = Bytes.length buffer in let try_to_output used_out = if used_out > 0 then (`output (Ok (Bytes.To_string.sub zlib_write_buffer ~pos:0 ~len:used_out))) else (`not_ready) in let (finished, used_in, used_out) = Zlib.inflate zstream buffer 0 len zlib_write_buffer 0 zlib_buffer_size Zlib.Z_SYNC_FLUSH in if used_in < len then ( if finished then ( match format with | `gzip when len - used_in >= 8 -> (* The 8-bytes CRC must be skipped then another Gzip header + stream can follow *) let continue_after_gzip = len - used_in > 8 in if continue_after_gzip then Buffer.add_string in_buffer (Bytes.To_string.sub buffer ~pos:(used_in + 8) ~len:(len - used_in - 8)); `finished_gzip (try_to_output used_out) | `gzip -> Buffer.add_string in_buffer Bytes.To_string.(sub buffer ~pos:used_in ~len:(len - used_in)); try_to_output used_out | _ -> `error (`garbage_at_end_of_compressed_data Bytes.To_string.(sub buffer ~pos:used_in ~len:(len - used_in))) ) else ( Buffer.add_string in_buffer Bytes.To_string.(sub buffer ~pos:used_in ~len:(len - used_in)); try_to_output used_out ) ) else try_to_output used_out let unzip ?(format=`raw) ?(zlib_buffer_size=Default.zlib_buffer_size) () = let zstream = ref (Zlib.inflate_init false) in let in_buffer = Buffer.create 42 in let zlib_write_buffer = Bytes.create zlib_buffer_size in let current_state = ref (match format with `gzip -> `gzip_header | `raw -> `inflate) in let rec next stopped = let buffered = Buffer.contents_bytes in_buffer in let len = Bytes.length buffered in Buffer.clear in_buffer; begin match len with | 0 -> if stopped then `end_of_stream else `not_ready | _ -> begin match !current_state with | `inflate -> begin try let inflation = inflate_as_much_as_possible in_buffer buffered !zstream zlib_write_buffer zlib_buffer_size format in begin match inflation with | `output o -> `output o | `error e -> `output (Error e) | `not_ready -> `not_ready | `finished_gzip out -> current_state := `gzip_header; zstream := Zlib.inflate_init false; out end with | e -> `output (Error (`zlib (Exn.to_string e))) end | `gzip_header -> begin try match try_skip_gzip_header_exn buffered with | Ok bytes_read -> current_state := `inflate; Buffer.add_string in_buffer Bytes.To_string.(sub buffered ~pos:bytes_read ~len:(len - bytes_read)); next stopped | Error e -> `output (Error e) with _ -> Buffer.add_bytes in_buffer buffered; `not_ready end end end in Tfxm.make_result () ~feed:(fun string -> Buffer.add_string in_buffer string;) ~next let gzip_default_header = (* ID1, Id2, compr meth, flags, mtime (4 bytes), xflags, OS (unknown) *) "\x1F\x8B\x08\x00\ \x00\x00\x00\x00\ \x00\xff" let bytes_empty () = Bytes.make 0 ' ' let zip ?(format=`raw) ?(level=Default.level) ?(zlib_buffer_size=Default.zlib_buffer_size) () = let zstream = ref (Zlib.deflate_init level false) in let in_buffer = Buffer.create 42 in let zlib_write_buffer = Bytes.create zlib_buffer_size in let state = ref (match format with `raw -> `deflating | `gzip -> `gzip_header) in let this_is_the_end = ref false in let update_crc, output_crc = match format with | `raw -> ((fun _ _ -> ()), (fun () -> bytes_empty ())) | `gzip -> let gzip_crc = ref 0l in let gzip_size = ref 0l in ((fun buf used_in -> gzip_crc := Zlib.update_crc !gzip_crc buf 0 used_in; gzip_size := Int32.(!gzip_size + (of_int_exn used_in)); ()), (fun () -> let buf = Bytes.create 8 in Binary_packing.pack_signed_32 ~byte_order:`Little_endian ~pos:0 ~buf !gzip_crc; Binary_packing.pack_signed_32 ~byte_order:`Little_endian ~pos:4 ~buf !gzip_size; buf)) in let next stopped = match state.contents with | `gzip_header -> state := `deflating; `output gzip_default_header | `deflating -> let buffered = Buffer.contents_bytes in_buffer in begin match Bytes.length buffered with | 0 -> if stopped then begin if !this_is_the_end then `end_of_stream else begin let (_, _, used_out) = Zlib.deflate !zstream (bytes_empty ()) 0 0 zlib_write_buffer 0 zlib_buffer_size Zlib.Z_FINISH in let to_output = if used_out < zlib_buffer_size then ( this_is_the_end := true; Zlib.deflate_end !zstream; (Bytes.To_string.sub zlib_write_buffer ~pos:0 ~len:used_out) ^ (Bytes.to_string (output_crc ())) ) else ( Bytes.To_string.sub zlib_write_buffer ~pos:0 ~len:used_out ) in `output to_output end end else `not_ready | len -> Buffer.clear in_buffer; let (_, used_in, used_out) = Zlib.deflate !zstream buffered 0 len zlib_write_buffer 0 zlib_buffer_size (* Zlib.Z_NO_FLUSH *) Zlib.Z_SYNC_FLUSH in update_crc buffered used_in; if used_in < len then (Buffer.add_subbytes in_buffer buffered ~pos:used_in ~len:(Bytes.length buffered - used_in)); if used_out > 0 then `output Bytes.To_string.(sub zlib_write_buffer ~pos:0 ~len:used_out) else `not_ready end in Tfxm.make () ~feed:(fun string -> Buffer.add_string in_buffer string;) ~next end let unzip_in_channel ?format ?zlib_buffer_size ?buffer_size inp = let t = Transform.unzip ?format ?zlib_buffer_size () in Tfxm.in_channel_strings_to_stream ?buffer_size inp t let zip_in_channel ?format ?zlib_buffer_size ?level ?buffer_size inp = let t = Transform.zip ?format ?zlib_buffer_size ?level () in Tfxm.in_channel_strings_to_stream ?buffer_size inp t exception Error of Error.unzip let error_to_exn e = Error e let unzip_in_channel_exn ?format ?zlib_buffer_size ?buffer_size inp = Stream.result_to_exn ~error_to_exn (unzip_in_channel ?format ?zlib_buffer_size ?buffer_size inp)
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