Get query sequence at specified positions in ref (bio::perl)

[obk]

Hi,
I'm trying to get the bases from a query that aligns to a specified location in the reference sequence.

For example, given the three alignments below,

     12345678
Ref1 ACGTACGT
     |||||| |
Qry1 ACGTA[COLOR="Red"]CT[/COLOR]T (Read is has a mismatch)

     12345678
Ref1 ACGTACGT
     | ||| ||
Qry2 A-GTA[COLOR="red"]GG[/COLOR]T (Read has a deletion and a mismatch)

     1 2345678
Ref1 A-CGTACGT
     | |||| ||
Qry3 AACGTA[COLOR="red"]AG[/COLOR]T (Read has an insertion and a mismatch)

I want to do something like (I'm using Bio::Perl and Bio:B::Sam)

my $start = 6;
my $end = 7;
$sam->fetch('Ref1',
 sub
 {
    my $a = shift;
    print $a->query->name,"\t";
    print $a->[B][COLOR="DarkRed"]some_magical_function[/COLOR][/B]($start,$end),"\n";
 });

... which should output

Qry1  CT
Qry2  GG
Qry3  AG

I suppose this can be achieved by parsing the cigar string or the padded_alignment (($ref,$matches,$query)=$a->padded_alignment;), but was wondering if there is a function that does this already.

Thanks.

[obk]

In case anyone is interested in this problem: see http://seqanswers.com/forums/showthread.php?p=88600