Bioperl: Something wrong get_all_primary_ids() ?

[Ewan Birney]

On Tue, 13 Jun 2000, Kris Boulez wrote:

> When using the get_all_primary_ids() method on a Bio::Index object I got
> back less id's then expected. Looking at the code in Bio::Index::AbstractSeq
> 
>     my( %bytepos );
>    while (my($id, $rec) = each %$db) {
>        my ($file, $begin, $end) = $self->unpack_record( $rec );
>        $bytepos{$begin} = $id;
>    }
> 
>    return values %bytepos;
> 
> I think $begin is not unique enough as key to %bytepos (same place in
> multiple files). Wouldn't it be better to replace this with


Good spot Kris. It should be

     "$file:$bytepos" 

This is because a single sequence could be indexed under more than one
identifier.

I have made this change on the 06 stable branch and main trunk - James -
you might want to code review this. ;)


> 
>     my( %bytepos );
>     my ($t);
>    while (my($id, $rec) = each %$db) {
>        my ($file, $begin, $end) = $self->unpack_record( $rec );
>        $bytepos{++$t} = $id;
>    }
> 
>    return values %bytepos;
> 
> It might be asked if (in this case) an array is not a better data structure.
> 
> 
> P.S. I'm hoping I'm not making a fool of me by overlooking something
> simple :).
> 
> Kris,
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