I have just begun exploring Lincoln Stein's excellent Bio::DB::Bam perl module and have an elementary question. Is it possible to edit values of an Bio::DB::Bam::Alignment alignment object?

Here is a dead simple script that just copies a bam file.

my $bam = Bio::DB::Bam->open("in.bam") ;
my $fix = Bio::DB::Bam->open("out.bam", "w" ) ;

my $header = $bam->header();
$fix->header_write($header);

while (my $align = $bam->read1 ) {
  # EDIT BAM FIELDS HERE
  $fix->write1($align);
}

What I want to do is edit some of the fields before writing them. For example, for each alignment, I can access the CIGAR field with $align->cigar_str or $align->cigar_array and I can get the sequence of the read with $align->qseq -- but is there a way I can change these values before writing them to the new file?