Comments on: 454 sequencing and parsing the SFF binary format http://blog.malde.org/index.php/2008/11/14/454-sequencing-and-parsing-the-sff-binary-format/ bioinformatics and haskell Sun, 04 Jul 2010 19:06:47 +0000 http://wordpress.org/?v=2.9.2 hourly 1 By: sof http://blog.malde.org/index.php/2008/11/14/454-sequencing-and-parsing-the-sff-binary-format/comment-page-1/#comment-137 sof Sun, 16 Nov 2008 17:49:00 +0000 http://blog.malde.org/index.php/2008/11/14/454-sequencing-and-parsing-the-sff-binary-format/#comment-137 Yes, a wibble :) That's good to know and sign of GHC doing its job well, but to remove the doubt, doing it manually has its merit (beyond code clarity.) Yes, a wibble :) That’s good to know and sign of GHC doing its job well, but to remove the doubt, doing it manually has its merit (beyond code clarity.)

]]> By: ketil http://blog.malde.org/index.php/2008/11/14/454-sequencing-and-parsing-the-sff-binary-format/comment-page-1/#comment-136 ketil Sat, 15 Nov 2008 18:14:54 +0000 http://blog.malde.org/index.php/2008/11/14/454-sequencing-and-parsing-the-sff-binary-format/#comment-136 Yes, I should have thought of that. Just tried it, but it doesn't make any difference to performance, so I guess GHC is already doing the right thing here. Still, I think the code is clearer, so I kept your suggestion. Thanks! Yes, I should have thought of that. Just tried it, but it doesn’t make any difference to performance, so I guess GHC is already doing the right thing here. Still, I think the code is clearer, so I kept your suggestion. Thanks!

]]> By: sof http://blog.malde.org/index.php/2008/11/14/454-sequencing-and-parsing-the-sff-binary-format/comment-page-1/#comment-135 sof Sat, 15 Nov 2008 16:51:02 +0000 http://blog.malde.org/index.php/2008/11/14/454-sequencing-and-parsing-the-sff-binary-format/#comment-135 Nice writeup of optimisation steps & reasoning. Simple improvement to 'showread' would be to manually deforest using zipWith3: showread :: CommonHeader -> ReadBlock -> [ByteString] showread h rd = zipWith3 (\ p c v -> B.concat [ rn,t,B.pack (show p),t , B.cons c t,fi v]) [(1::Int)..] (unpack $ flow h) (flowgram rd) where rn = read_name $ read_header rd Nice writeup of optimisation steps & reasoning. Simple improvement to ’showread’ would be to manually deforest using zipWith3:

showread :: CommonHeader -> ReadBlock -> [ByteString]
showread h rd =
zipWith3 (\ p c v ->
B.concat [ rn,t,B.pack (show p),t
, B.cons c t,fi v])
[(1::Int)..]
(unpack $ flow h)
(flowgram rd)
where
rn = read_name $ read_header rd

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