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lib/GenOO/Data/File/SAM.pm  view on Meta::CPAN

# POD documentation - main docs before the code

=head1 NAME

GenOO::Data::File::SAM - Object implementing methods for accessing SAM formatted files

=head1 SYNOPSIS

    # Object that manages a sam file.

    # To initialize
    my $sam_file = GenOO::Data::File::SAM->new(
        file            => undef,
    );


=head1 DESCRIPTION

    This object implements methods to read a sam file line by line.

=head1 EXAMPLES

    # Create object
    my $sam_file = GenOO::Data::File::SAM->new(
          file => 't/sample_data/sample.sam.gz'
    );

    # Read one record at a time
    my $sam_record = $sam_file->next_record();

=cut

# Let the code begin...

package GenOO::Data::File::SAM;
$GenOO::Data::File::SAM::VERSION = '1.5.2';

#######################################################################
#######################   Load External modules   #####################
#######################################################################
use Modern::Perl;
use autodie;
use Moose;
use namespace::autoclean;


#######################################################################
#######################   Interface attributes   ######################
#######################################################################
has 'file' => (
	isa      => 'Maybe[Str]', # undef value makes the parser read from STDIN
	is       => 'ro',
	required => 1,
);

has 'records_read_count' => (
	traits  => ['Counter'],
	is      => 'ro',
	isa     => 'Num',
	default => 0,
	handles => {
		_inc_records_read_count   => 'inc',
		_reset_records_read_count => 'reset',
	},
);

has 'records_class' => (
	is        => 'ro',
	default   => 'GenOO::Data::File::SAM::Record',
);

#######################################################################
########################   Private attributes   #######################
#######################################################################
has '_filehandle' => (
	is        => 'ro',
	builder   => '_open_filehandle',
	init_arg  => undef,
	lazy      => 1,
);

has '_is_eof_reached' => (
	traits  => ['Bool'],
	is      => 'rw',
	isa     => 'Bool',
	default => 0,
	handles => {
		_set_eof_reached   => 'set',
		_unset_eof_reached => 'unset',
		_eof_not_reached   => 'not',
	},
);

has '_cached_header_lines' => (
	traits  => ['Array'],
	is      => 'ro',
	default => sub { [] },
	handles => {
		_all_cached_header_lines    => 'elements',
		_add_header_line_in_cache   => 'push',
		_shift_cached_header_line   => 'shift',