[Biojava-l] reading nib sequence files

[mark.schreiber at group.novartis.com]

I'd need to brush up on my nio, and my c !





Thomas Down <td2 at sanger.ac.uk>
01/24/2005 04:34 PM

 
        To:     "Richard HOLLAND" <hollandr at gis.a-star.edu.sg>
        cc:     "<baggott2 at llnl.gov>", biojava-list List <biojava-l at biojava.org>, Mark 
Schreiber/GP/Novartis at PH
        Subject:        Re: [Biojava-l] reading nib sequence files



On 24 Jan 2005, at 02:48, Richard HOLLAND wrote:

> It's a compressed binary format. I doubt BioJava would be able to read
> it without a lot of effort as the current parser framework is set up 
> for
> text input only.

Nib support probably wouldn't fit into the text-oriented parsing 
framework, but I'm sure it could be supported somehow if there was 
demand.  A quick google doesn't turn up any format documentation, but 
Jim Kent's IO code is at:

           http://www.soe.ucsc.edu/~kent/src/unzipped/lib/nib.c

One interesting way to handle this might be to open the nib file as a 
MappedByteBuffer, and back a SymbolList directly using that -- 
potentially giving us an efficient way of working with huge sequences.. 
  Any interest in that?

           Thomas.