package Bio::DB::Bam::PileupWrapper;
#$Id$

=head1 NAME

Bio::DB::Bam::PileupWrapper -- Add high-level methods to Bio::DB::Bam::Pileup

=head1 SYNOPSIS

See L<Bio::DB::Sam/The generic fetch() and pileup() methods> for usage of the pileup() method.

=head1 DESCRIPTION

See L<Bio::DB::Bam::Pileup> for documentation of this object's
methods. This class is used by the high-level API to return
Bio::DB::Bam::AlignWrapper objects from the call to alignment() rather
than Bio::DB::Bam::Alignment.

=head1 SEE ALSO

L<Bio::Perl>, L<Bio::DB::Sam>, L<Bio::DB::Bam::Constants>

=head1 AUTHOR

Lincoln Stein E<lt>lincoln.stein@oicr.on.caE<gt>.
E<lt>lincoln.stein@bmail.comE<gt>

Copyright (c) 2009-2015 Ontario Institute for Cancer Research.

This package and its accompanying libraries are free software; you can
redistribute it and/or modify it under the terms of the Artistic
License 2.0, the Apache 2.0 License, or the GNU General Public License
(version 1 or higher).  Refer to LICENSE for the full license text.

=cut

use strict;
use Bio::DB::Bam::AlignWrapper;

our $AUTOLOAD;
use Carp 'croak';

sub new {
    my $package = shift;
    my ($align,$sam) = @_;
    return bless {sam    => $sam,
		  pileup => $align},ref $package || $package;

}

sub AUTOLOAD {
  my($pack,$func_name) = $AUTOLOAD=~/(.+)::([^:]+)$/;
  return if $func_name eq 'DESTROY';

  no strict 'refs';
  $_[0] or die "autoload called for non-object symbol $func_name";
  croak qq(Can't locate object method "$func_name" via package "$pack")
      unless $_[0]->{pileup}->can($func_name);

  *{"${pack}::${func_name}"} = sub { shift->{pileup}->$func_name(@_) };

  shift->$func_name(@_);
}

sub can {
    my $self = shift;
    return 1 if $self->SUPER::can(@_);
    return $self->{pileup}->can(@_);
}

sub alignment {
    my $self = shift;
    return Bio::DB::Bam::AlignWrapper->new($self->{pileup}->b,$self->{sam});
}

1;