File Coverage

lib/App/Sandy/Role/IO.pm

Criterion	Covered	Total	%
statement	25	29	86.2
branch	5	12	41.6
condition			n/a
subroutine	7	8	87.5
pod	0	4	0.0
total	37	53	69.8

package App::Sandy::Role::IO;
# ABSTRACT: Input and output custom wrappers.

use App::Sandy::Base 'role';
use App::Sandy::BGZF;
use IO::Compress::Gzip '$GzipError';
use PerlIO::gzip;

our $VERSION = '0.24'; # VERSION

sub with_open_r {
	my ($self, $file) = @_;

	my $fh;
	my $mode = $file =~ /\.gz$/ ? "<:gzip" : "<";

	open $fh, $mode => $file
		or die "Not possible to read $file: $!\n";

	return $fh;
}

sub with_open_w {
	my ($self, $file, $level) = @_;

	my $fh;

	if ($level) {
		$fh = IO::Compress::Gzip->new($file, -Level => $level)
			or die "Not possible to create $file: $GzipError\n";
	} else {
		open $fh, '>' => $file
			or die "Not possible to create $file: $!\n";
	}

	return $fh;
}

sub with_open_a {
	my ($self, $file) = @_;

	open my $fh, '>>' => $file
		or die "Not possible to append to $file: $!\n";

	return $fh;
}

sub with_open_bam_w {
	my ($self, $file, $level) = @_;
	my $fh = App::Sandy::BGZF->new_filehandle($file, $level);
	return $fh;
}

__END__

=pod

=encoding UTF-8

=head1 NAME

App::Sandy::Role::IO - Input and output custom wrappers.

=head1 VERSION

version 0.24

=head1 AUTHORS

=over 4

=item *

Thiago L. A. Miller <[e-mail]>

=item *

J. Leonel Buzzo <[e-mail]>

=item *

Felipe R. C. dos Santos <[e-mail]>

=item *

Helena B. Conceição <[e-mail]>

=item *

Rodrigo Barreiro <[e-mail]>

=item *

Gabriela Guardia <[e-mail]>

=item *

Fernanda Orpinelli <[e-mail]>

=item *

Rafael Mercuri <[e-mail]>

=item *

Rodrigo Barreiro <[e-mail]>

=item *

Pedro A. F. Galante <[e-mail]>

=back

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2023 by Teaching and Research Institute from Sírio-Libanês Hospital.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut