/usr/share/perl5/Bio/Tradis/CommandLine/CheckTags.pm is in bio-tradis 1.3.3+dfsg-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 | package Bio::Tradis::CommandLine::CheckTags;
# ABSTRACT: Check for presence of tr tag in BAM file
=head1 SYNOPSIS
Check for presence of tr tag in BAM file
=cut
use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd 'abs_path';
use Bio::Tradis::DetectTags;
has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
has 'bamfile' => ( is => 'rw', isa => 'Str', required => 0 );
has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );
sub BUILD {
my ($self) = @_;
my (
$bamfile, $help, $samtools_exec
);
GetOptionsFromArray(
$self->args,
'b|bamfile=s' => \$bamfile,
'h|help' => \$help,
'samtools_exec=s' => \$samtools_exec,
);
$self->bamfile(abs_path($bamfile)) if ( defined($bamfile) );
$self->help($help) if ( defined($help) );
$self->samtools_exec($samtools_exec) if ( defined($samtools_exec) );
# print usage text if required parameters are not present
($bamfile) or die $self->usage_text;
}
sub run {
my ($self) = @_;
if ( defined( $self->help ) ) {
$self->usage_text;
}
my $tagcheck = Bio::Tradis::DetectTags->new(bamfile => $self->bamfile, samtools_exec => $self->samtools_exec );
print $tagcheck->tags_present . "\n";
}
sub usage_text {
print <<USAGE;
Check for the existence of tradis tags in a bam
Usage: check_tags -b file.bam
Options:
-b : bam file with tradis tags
USAGE
exit;
}
__PACKAGE__->meta->make_immutable;
no Moose;
1;
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