Re: De referencing

[poj]

From the docs;

$alignment = $bam->read1()
Read one alignment from the BAM file and return it as a Bio::DB::Bam::
+Alignment object.

You need to use the methods in Bio::DB::Bam::Alignment to access the information. For example

 while (my $align = $bam->read1) {
    my $seqid  = $align->seq_id;
    my $start  = $align->start;
    my $end    = $align->end;
    my $strand = $align->strand;
    my $ref_dna= $align->dna;
}

poj