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
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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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