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

# POD documentation - main docs before the code

=head1 NAME

GenOO::Data::File::SAM::Record - Object representing a record of a sam file

=head1 SYNOPSIS

    # Object representing a record of a sam file 

    # To initialize 
    my $sam_record = GenOO::Data::File::SAM::Record->new(
        fields => [qname,flag, rname, pos, mapq, cigar,
                   rnext, pnext, tlen, seq, qual, tags]
    );


=head1 DESCRIPTION

    This object represents a record of a sam file and offers methods for accessing the different attributes.
    It implements several additional methods that transform original attributes in more manageable attributes.
    eg. from the FLAG attribute the actual strand is extracted etc.

=head1 EXAMPLES

    # Check if the record corresponds to a match
    my $mapped = $sam_record->is_mapped;
    
    # Check if the record corresponds to a non match
    my $unmapped = $sam_record->is_unmapped;
    
    # Parse the FLAG attribute and return 1 or -1 for the strand
    my $strand = $sam_record->strand;

=cut

# Let the code begin...

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

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


#######################################################################
#######################   Interface attributes   ######################
#######################################################################
has 'fields' => (
	traits  => ['Array'],
	is      => 'ro',
	isa     => 'ArrayRef[Str]',
	default => sub { [] },
	handles => {
		all_fields    => 'elements',
		add_field     => 'push',
		map_fields    => 'map',
		filter_fields => 'grep',
		find_field    => 'first',
		get_field     => 'get',
		join_fields   => 'join',
		count_fields  => 'count',
		has_fields    => 'count',
		has_no_fields => 'is_empty',
		sorted_fields => 'sort',
	},
	required => 1,
);

has 'tags' => (
	is        => 'ro',
	builder   => '_read_tags',
	init_arg  => undef,
	lazy      => 1,
);

has 'alignment_length' => (
	is        => 'ro',
	builder   => '_calculate_alignment_length',
	init_arg  => undef,
	lazy      => 1,
);

has 'start' => (
	is        => 'ro',
	builder   => '_calculate_start',
	init_arg  => undef,
	lazy      => 1,
);

has 'stop' => (
	is        => 'ro',
	builder   => '_calculate_stop',
	init_arg  => undef,
	lazy      => 1,
);

has 'strand' => (
	is        => 'ro',
	builder   => '_calculate_strand',