#!/usr/bin/env perl
use strict;
use warnings FATAL => 'all';

use File::Copy;
use Getopt::Std;
use Pod::Usage;

use Bio::GFF3::Transform::SyncDirectives 'gff3_add_sync_directives';

my %opt;
getopts('i',\%opt) or pod2usage('invalid options');

@ARGV or pod2usage('must provide one or more filenames');

if( $opt{i} ) {
    for my $file ( @ARGV ) {
        -r $file or die "cannot open file '$file' for reading\n";
        my $temp_out = File::Temp->new;
        gff3_add_sync_directives( $temp_out, $file );
        $temp_out->close;
        move( "$temp_out", $file ) or die "cannot overwrite '$file': $!\n";
    }
} else {
    gff3_add_sync_directives( \*STDOUT, @ARGV );
}

# PODNAME: gff3_insert_sync_directives
# ABSTRACT: efficiently insert sync (###) directives into GFF3, printing to stdout


__END__
=pod

=encoding utf-8

=head1 NAME

gff3_insert_sync_directives - efficiently insert sync (###) directives into GFF3, printing to stdout

=head1 USAGE

    gff3_insert_sync_directives file file ... > with_syncs.gff3

Note: because GFF3 is read in reverse order, cannot operate on
streamed input.  So no stdin, sorry.

=head2 Options

=over 4

=item -i

Instead of printing to standard output, modify each file in-place.
Similar to perl's -i switch.

=back

=head1 AUTHOR

Robert Buels <rmb32@cornell.edu>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2012 by Robert Buels.

This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.

=cut