use Bio::DB::Sam;
$fh = Bio::DB::Sam->new(-fasta=> "fasta file", -bam  =>"bam input file");
my $header = $fh->header();
my $bam_out = Bio::DB::Bam->open("bam out file", "w+");
my @alignments = $fh->features();
for my $align (@alignments) {
	my $query = $align->qname;
	my $target = $align->seq_id;
        my $is_unmapped = $align->unmapped;
	unless ($in_unmapped) {
		$bam_out->write1($align);       
       }
}