| 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 |
|
670
|
1 |
1 |
if (exists $args{'columns'}) { } |
|
|
0 |
1 |
elsif (exists $args{'datasets'}) { } |
|
678
|
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 $args{'ucsc'}) { } |
|
687
|
0 |
0 |
unless ($self->extension =~ /g[tf]f/) |
|
689
|
0 |
0 |
$args{'gff'} == 3 ? : |
|
|
0 |
0 |
$args{'gff'} == 2.5 ? : |
|
694
|
0 |
1 |
unless ($args{'bed'} =~ /^\d{1,2}$/ and $args{'bed'} >= 3) |
|
699
|
0 |
1 |
unless ($self->extension =~ /bed|peak/) |
|
706
|
0 |
0 |
unless ($u) |
|
710
|
0 |
0 |
unless ($self->extension =~ /ucsc|ref+lat|genepred/) |
|
717
|
0 |
0 |
if (exists $args{'gz'} and $args{'gz'} and not $self->extension =~ /gz$/) |
|
726
|
1 |
1 |
unless $self->feature |
|
735
|
0 |
1 |
unless ($filename) |
|
739
|
0 |
1 |
if ($filename eq $self->filename) |
|
746
|
0 |
1 |
unless my $Dup = $self->new("out", $filename, "columns", $columns) |
|
773
|
0 |
4 |
unless $name |
|
774
|
0 |
4 |
unless ($self->mode) |
|
778
|
0 |
4 |
if (defined $self->{'fh'}) |
|
791
|
0 |
4 |
if exists $self->{'column_indices'} |
|
792
|
0 |
4 |
if ($self->gff or $self->bed or $self->ucsc or $self->vcf) |
|
801
|
0 |
0 |
unless ($self->mode) |
|
804
|
0 |
0 |
if (defined $self->{'fh'}) |
|
809
|
0 |
0 |
unless defined $index |
|
824
|
0 |
201 |
if ($self->{'mode'}) |
|
829
|
5 |
196 |
unless my $line = $self->{'fh'}->getline |
|
831
|
0 |
196 |
if (substr($line, 0, 1) eq "#") |
|
855
|
0 |
78 |
unless ($self->{'mode'}) |
|
860
|
2 |
76 |
unless (defined $self->{'fh'}) |
|
863
|
0 |
2 |
unless ($newfile) |
|
868
|
0 |
2 |
if ($newfile ne $self->filename) |
|
873
|
0 |
2 |
unless my $fh = $self->open_to_write_fh($newfile, undef, 1) |
|
880
|
39 |
39 |
if ($data_ref eq 'Bio::ToolBox::Data::Feature') { } |
|
|
39 |
0 |
elsif ($data_ref eq 'ARRAY') { } |
|
891
|
0 |
0 |
unless ($data =~ /\n$/) |
|
902
|
0 |
0 |
unless (ref $code eq "CODE") |