[Bioperl-l] sequencer datafiles, qualities, and other things

[Chad Matsalla]

Hi all,

I committed the things I said I would commit so if anybody who works with
qualities, phredfiles, or scf's is lurking here please check them out and
let me know what you think.

They are documented and tested- I submitted the tests and some sample
files (.phd,.qual,.scf) for the tests but I wasn't sure where the sample
files should go- t/ or examples/ ? I put them in t/ but I'm not married to
the idea.

The scf parser is a bit rough and is full of debugging information. I
wasn't comfortable with its quality so I committed it as csmscf.pm (csm is
me). Hopefully I can get a bit of feedback.

I also have a .abi parser that I've been using lately to get trace data
from abi 377 and 3700 sequence datafiles. It resembles SeqIO::csmscf.pm
in that it massages the binary data into more immediately useful objects.
It isn't complete but if there is anybody desperate for that kind of
functionality let me know but it might be easier to get a program like
phred to convert the .abi to a .scf and then work with that.

Chad Matsalla