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=head1 DESCRIPTION

Annotate alignments in a database table with regions from a BED/SAM file.
Adds a user defined column that will be NOT NULL if an alignment is contained within a region from the file and NULL otherwise.

=head1 OPTIONS

  Input options for library.
    --driver <Str>         driver for database connection (eg. mysql,
                           SQLite).
    --database <Str>       database name or path to database file for file
                           based databases (eg. SQLite).
    --table <Str>          database table.
    --host <Str>           hostname for database connection.
    --user <Str>           username for database connection.
    --password <Str>       password for database connection.
    --records_class <Str>  type of records stored in database.
    --filter <Filter>      filter library. May be used multiple times.
                           Syntax: column_name="pattern"
                           e.g. keep reads with deletions AND not repeat
                                masked AND longer than 31
                                --filter deletion="def" 
                                --filter rmsk="undef" .
                                --filter query_length=">31".
                           Operators: >, >=, <, <=, =, !=, def, undef

  Other input
    --a_type <Str>         type of file with annotation regions (i.e. BED,
                           SAM).
    --a_file <Str>         file with annotation regions.

  Database options.
    --drop                 drop column if it already exists (not
                           supported in SQlite).

  Other options.
    --column <Str>         name for the new annotation column.
    --both_strands         annotate both strands irrespective of the
                           region strand specified in the file. May be
                           useful for repeats where only one strand is
                           usually provided.
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message

=cut

package CLIPSeqTools::PreprocessApp::annotate_with_file;
$CLIPSeqTools::PreprocessApp::annotate_with_file::VERSION = '1.0.0';

# Make it an app command
use MooseX::App::Command;
extends 'CLIPSeqTools::PreprocessApp';


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


#######################################################################
#######################   Command line options   ######################
#######################################################################
option 'a_type' => (
	is            => 'rw',
	isa           => 'Str',
	default       => 'BED',
	documentation => 'type of file with annotation regions (ie. BED, SAM).',
);

option 'a_file' => (
	is            => 'rw',
	isa           => 'Str',
	required      => 1,
	documentation => 'file with annotation regions.',
);

option 'column' => (
	is            => 'rw',
	isa           => 'Str',
	required      => 1,
	documentation => 'name for the new annotation column.',
);

option 'drop' => (
	is            => 'rw',
	isa           => 'Bool',
	documentation => 'drop columns if they already exist (not supported in SQlite).',
);

option 'both_strands' => (
	is            => 'rw',
	isa           => 'Bool',
	documentation => 'annotate both strands irrespective of the region strand specified in the file. May be useful for repeats where only one strand is usually provided.',
);


#######################################################################
##########################   Consume Roles   ##########################
#######################################################################
with 
	"CLIPSeqTools::Role::Option::Library" => {
		-alias    => { validate_args => '_validate_args_for_library' },
		-excludes => 'validate_args',
	};


#######################################################################
########################   Interface Methods   ########################
#######################################################################
sub validate_args {
	my ($self) = @_;
	
	$self->_validate_args_for_library;
}

sub run {
	my ($self) = @_;