[Bioperl-l] Staden io_lib support

[Aaron J Mackey]

OK, after a flurry of bug-fix commits, I think things are pretty stable.
Try it out, let me know what breaks.

Note that ztr will read ztr files compressed at any level; to write files
at a specific compression level, you need to specify the --compression
option to new (default is 2; valid values are 1..3).  You'll of course
also need zlib installed for io_lib to even give you this format as an
option.

I am having one problem that I'd appreciate help with: For some reason,
the normal:

$in = new Bio::SeqIO -format => "abi", -file => "readtest.abi";

Doesn't work (Bio::SeqIO::abi doesn't properly load staden::read) ... but
if I do:

$in = new Bio::SeqIO::abi  -file => "readtest.abi";

Then it works fine.  I can't figure out why SeqIO's load_format isn't
doing the job well enough ... if I have SeqIO attempt to preload
staden::read (via it's BEGIN sub) everything works fine (checked in, but
not happy about it).

Well unless there's further discussion, I now return to parsing PAML ...

-Aaron

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu