[Biojava-dev] SCF Issues and leading up to 1.4 release

[Andrew Yates]

Hi guys,

First post on the dev list here but with talk of a 1.4 release coming up 
soon at BOSC it reminded me that there are certain bugs in the SCF 
parser code. The bug is with the wrapping of byte/short values into the 
int[] output. I've seen cases where the current parser generates trace 
files with an intensity of 65000 (slightly over the range ABI machines 
can handle by about 30000) when dealing with byte centric files (SCF can 
write values in byte if the delta delta values do not exceed unsigned 
byte boundries).

I've developed a fix for it and have the new source available for it 
(and this code has been tested & running flawlessly in our program for 
about 6 months) but I thought it best to try to shoehorn it in before a 
1.4 release hopefully and if not get it in so it gets into any update 
release.

What's the best way around this? I don't mind editing the CVS entry but 
since this is my contribution to biojava I know I wouldn't be happy from 
an admin point of view.

Cheers,

Andy Yates
~~~~~~~~~~
Computer Biologist
Cancer Genome Project
Wellcome Trust Sanger Institute


P.S. Good conference guys