[Bioperl-l] sequence trace index data

[Chad Matsalla]

Greetings all,

Does anybody have any opinion on how trace index points should be
stored?

I am talking about the following situation:

1. I have an ab1-formated trace file
2. I call the bases using phred
3. Using SeqIO, I gather the phred data from the .phd.1 file (generated
by phred.
4. I pass what data into Bio::Tools::Alignment::Trim.pm and get what it
thinks are the boundries for good sequence.
5. I then take a slice of the .phd.1 file and pass it into scf.pm's
write_seq(Bio::Seq::SeqWithQuality) to generate a new scf representing
just the good region.


The problem as it stands is that phd.pm igores trace indices when it
reads in .phd files. I can fix that easily enough (I already have) but
the larger question is:
Where should trace index data go?

I have placed it as an array in Bio::Seq::SeqWithQuality for now because
I have to blow this project out the door but if anybody has better
ideas, please let me know.

Chad Matsalla