[Bioperl-l] SeqIO/scf.pm bug (with fix)

[Heikki Lehvaslaiho]

I've commmited the fix into the main trunk. 

Thanks, Tony.

	-Heikki

On Tue, 2002-10-29 at 15:57, Tony Cox wrote:
> 
> There is a bug in the SeqIO SCF module that means that SCF files with low
> dynamic range data that have their trace data values encoded as 8-bit unsigned
> values (rather than the normal 16-bit) are incorrectly parsed. This caused the
> unpack function to overrun the data and extract garbage.
> 
> I'm hoping that somebody can add the patch below to the main trunck SeqIO/scf.pm
> module. Here is the diff to fix it:
> 
> 
> 147,151c158
> <             my $byte = "n";
> <             if ($self->{sample_size} == 1){
> <                 $byte = "c";
> <             }
> <               @read = unpack "${byte}${length}",$buffer;
> ---
> >                       @read = unpack "n$length",$buffer;
> 
> 
> regards
> 
> Tony
> 
> 
> ******************************************************
> Tony Cox			Email:avc@sanger.ac.uk
> Sanger Institute		WWW:www.sanger.ac.uk
> Wellcome Trust Genome Campus	Webmaster
> Hinxton				Tel: +44 1223 834244
> Cambs. CB10 1SA			Fax: +44 1223 494919
> ******************************************************
> 
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
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