line |
true |
false |
branch |
622
|
0 |
2 |
unless ($args{'in'} or $args{'out'}) |
626
|
0 |
28 |
if (defined $args{'in'} and defined $args{'out'}) |
636
|
26 |
2 |
if ($args{'in'}) { } |
|
2 |
0 |
elsif ($args{'out'}) { } |
640
|
0 |
26 |
unless ($filename) |
645
|
0 |
26 |
unless $self->open_to_read_fh |
669
|
1 |
1 |
if (exists $args{'columns'}) { } |
|
0 |
1 |
elsif (exists $args{'datasets'}) { } |
677
|
1 |
1 |
if (@columns) { } |
|
0 |
1 |
elsif (exists $args{'gff'} and $args{'gff'}) { } |
|
1 |
0 |
elsif (exists $args{'bed'} and $args{'bed'}) { } |
|
0 |
0 |
elsif (exists $args{'ucsc'} and $args{'ucsc'}) { } |
686
|
0 |
0 |
unless ($self->extension =~ /g[tf]f/) |
688
|
0 |
0 |
$args{'gff'} == 3 ? : |
|
0 |
0 |
$args{'gff'} == 2.5 ? : |
693
|
0 |
1 |
unless ($args{'bed'} =~ /^\d{1,2}$/ and $args{'bed'} >= 3) |
698
|
0 |
1 |
unless ($self->extension =~ /bed|peak/) |
705
|
0 |
0 |
unless ($u) |
709
|
0 |
0 |
unless ($self->extension =~ /ucsc|ref+lat|genepred/) |
716
|
0 |
0 |
if (exists $args{'gz'} and $args{'gz'} and not $self->extension =~ /gz$/) |
725
|
1 |
1 |
unless $self->feature |
734
|
0 |
1 |
unless ($filename) |
738
|
0 |
1 |
if ($filename eq $self->filename) |
745
|
0 |
1 |
unless my $Dup = $self->new('out', $filename, 'columns', $columns) |
772
|
0 |
4 |
unless $name |
773
|
0 |
4 |
unless ($self->mode) |
777
|
0 |
4 |
if (defined $self->{'fh'}) |
790
|
0 |
4 |
if exists $self->{'column_indices'} |
791
|
0 |
4 |
if ($self->gff or $self->bed or $self->ucsc or $self->vcf) |
800
|
0 |
0 |
unless ($self->mode) |
803
|
0 |
0 |
if (defined $self->{'fh'}) |
808
|
0 |
0 |
unless defined $index |
823
|
0 |
201 |
if ($self->{'mode'}) |
828
|
5 |
196 |
unless my $line = $self->{'fh'}->getline |
830
|
0 |
196 |
if (substr($line, 0, 1) eq '#') |
854
|
0 |
78 |
unless ($self->{'mode'}) |
859
|
2 |
76 |
unless (defined $self->{'fh'}) |
862
|
0 |
2 |
unless ($newfile) |
867
|
0 |
2 |
if ($newfile ne $self->filename) |
872
|
0 |
2 |
unless my $fh = $self->open_to_write_fh($newfile, undef, 1) |
879
|
39 |
39 |
if ($data_ref eq 'Bio::ToolBox::Data::Feature') { } |
|
39 |
0 |
elsif ($data_ref eq 'ARRAY') { } |
890
|
0 |
0 |
unless ($data =~ /\n$/) |
901
|
0 |
0 |
unless (ref $code eq 'CODE') |