[Bioperl-l] AlignIO test sending undefined val errors

[Jason Stajich]

Any complaints with the following changes:

I was getting errors from PrimarySeqI GCG_checksum
code would be changed to:
   foreach $char ( split(/[\.\-]*/, $seq)) {
	$index++;
>	$checksum += ($index * (unpack("c",$char) || 0) );
	if( $index ==  57 ) {
	    $index = 0;
	}
    }

from:
> $checksum += ($index * unpack("c",$char) );

was getting errors wih LargePrimarySeq on trying to close undef fh

added the ">" lines to DESTROY 
sub DESTROY {
    my $self = shift;
>    if( defined  $self->_fh ) {
	$self->_fh->close();
>    }
    unlink($self->_filename);
}

-Jason

Jason Stajich
jason@chg.mc.duke.edu
http://galton.mc.duke.edu/~jason/
(919)684-1806 (office) 
(919)684-2275 (fax) 
Center for Human Genetics - Duke University Medical Center
http://wwwchg.mc.duke.edu/