File Coverage

lib/App/SimulateReads/Command/QualityDB/Remove.pm

Criterion	Covered	Total	%
statement	3	15	20.0
branch	0	8	0.0
condition			n/a
subroutine	1	4	25.0
pod	3	3	100.0
total	7	30	23.3

package App::SimulateReads::Command::QualityDB::Remove;
# ABSTRACT: qualitydb subcommand class. Remove a quality profile from database.

use App::SimulateReads::Base 'class';

extends 'App::SimulateReads::Command::QualityDB';

our $VERSION = '0.06'; # VERSION

override 'opt_spec' => sub {
	super,
	'verbose|v',
	'quality-profile|q=s',
	'read-size|r=i'
};

sub validate_args {
	my ($self, $args) = @_;
	die "Too many arguments: '@$args'\n" if @$args;
}

sub validate_opts {
	my ($self, $opts) = @_;

	if (not exists $opts->{'quality-profile'}) {
		die "Option 'quality-profile' not defined\n";
	}

	if (not exists $opts->{'read-size'}) {
		die "Option 'read-size' not defined\n";
	}
}

sub execute {
	my ($self, $opts, $args) = @_;
	$LOG_VERBOSE = exists $opts->{verbose} ? $opts->{verbose} : 0;
	log_msg "Attempting to remove $opts->{'quality-profile'}:$opts->{'read-size'}";
	$self->deletedb($opts->{'quality-profile'}, $opts->{'read-size'});
	log_msg "Done!";
}

__END__

=pod

=encoding UTF-8

=head1 NAME

App::SimulateReads::Command::QualityDB::Remove - qualitydb subcommand class. Remove a quality profile from database.

=head1 VERSION

version 0.06

=head1 SYNOPSIS

 simulate_reads qualitydb remove -q <entry name> -r <size>

 Options:
  -h, --help               brief help message
  -M, --man                full documentation
  -v, --verbose            print log messages
  -q, --quality-profile    quality-profile name for the database [required]
  -r, --read-size          the read-size of the quality-profile [required, Integer]

=head1 DESCRIPTION

B<simulate_reads> will read the given input file and do something
useful with the contents thereof.

=head1 AUTHOR

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

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2017 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