test.pl

use Bio::DB::Sam;

# high level API
my $sam = Bio::DB::Sam->new(-bam  =>"data/ex1.bam",
                         -fasta=>"data/ex1.fa",
                         );

my @targets    = $sam->seq_ids;
my @alignments = $sam->get_features_by_location(-seq_id => 'seq2',
                                             -start  => 500,
                                             -end    => 800);

for my $a (@alignments) {
    # where does the alignment start in the reference sequence
    my $seqid  = $a->seq_id;
    my $start  = $a->start;
    my $end    = $a->end;
    my $strand = $a->strand;
    my $cigar  = $a->cigar_str;
    my $paired = $a->get_tag_values('PAIRED');

    # where does the alignment start in the query sequence
    my $query_start = $a->query->start;
    my $query_end   = $a->query->end;

    my $ref_dna   = $a->dna;        # reference sequence bases
    my $query_dna = $a->query->dna; # query sequence bases

    my @scores    = $a->qscore;     # per-base quality scores
    my $match_qual= $a->qual;       # quality of the match
}

my @pairs = $sam->get_features_by_location(-type   => 'read_pair',
                                        -seq_id => 'seq2',
                                        -start  => 500,
                                        -end    => 800);

for my $pair (@pairs) {
    my $length                    = $pair->length;   # insert length
    my ($first_mate,$second_mate) = $pair->get_SeqFeatures;
    my $f_start = $first_mate->start;
    # my $s_start = $second_mate->start;
}