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

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