dude .. you rock ... let me check it out ;^) Vasili On Fri, Jan 2, 2009 at 12:24 AM, Antoine Latter wrote:

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it is a bioinformatics standard .. . I am writing on this newsgroup in order to try to be objective to get a "correct" and elegant answer .. in any case I am helping on the bioinformatics code (you can see on Hackage). I am

On Jan 1, 2009 11:50pm, "Galchin, Vasili" wrote: trying to finish the 2Bit file format code ... it seems to me that bioinformatics as an area is not clearly defined .... e.g. it is unclear to me whether "offset" is a marshalled/serialized concept or or unmarshalled/unserialized concept ..... this distinction is very important .... I will have to think about more myself!

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Regards, Vasili

Here's some code using Data.Binary to store data as offsets into a byte array. I haven't tested it too much, so it may have bugs. Maybe there's some inspiration in there.

-Antoine

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import Data.Binary import Data.Binary.Get import Data.Binary.Put

import Data.ByteString.Lazy (ByteString) import qualified Data.ByteString.Lazy as B

data TestStruct = TestStruct { property1 :: ByteString , property2 :: ByteString , property3 :: ByteString } deriving Show

{-

The serialized format looks like (all big-endian):

* first offset into data block (Word32) * second offset into data block (Word32) * third offset into data block (Word32) * length of bnary data block (Word32) * binary data block (Arbitrary binary data)

-} instance Binary TestStruct where put struct = let data1 = property1 struct data2 = property2 struct data3 = property3 struct

dataBlock = data1 `B.append` data2 `B.append` data3

offset1 = 0 offset2 = offset1 + B.length data1 offset3 = offset2 + B.length data2

in do putWord32be $ fromIntegral offset1 putWord32be $ fromIntegral offset2 putWord32be $ fromIntegral offset3

putWord32be $ fromIntegral $ B.length dataBlock putLazyByteString dataBlock

get = do offset1 <- getWord32be offset2 <- getWord32be offset3 <- getWord32be

dataBlockLength <- getWord32be dataBlock <- B.drop (fromIntegral offset1) `fmap` getLazyByteString (fromIntegral dataBlockLength)

let (data1, rest1) = B.splitAt (fromIntegral $ offset2 - offset1) dataBlock (data2, rest2) = B.splitAt (fromIntegral $ offset3 - offset2 - offset1) rest1 data3 = rest2

return $ TestStruct data1 data2 data3 <<<<<