| line |
true |
false |
branch |
|
133
|
0 |
1 |
unless my $base = shift() |
|
137
|
0 |
1 |
unless -d $base and -w _ |
|
151
|
0 |
1 |
if @_ |
|
157
|
0 |
1 |
if @_ |
|
176
|
0 |
0 |
$options->{'visibility'} =~ /pack/i ? : |
|
177
|
0 |
0 |
$options->{'visibility'} =~ /pack/i ? : |
|
181
|
0 |
0 |
if (my $graph_type = $options->{'glyph'}) { } |
|
182
|
0 |
0 |
if ($graph_type =~ /box/) { } |
|
186
|
0 |
0 |
$graph_type =~ /density/ ? : |
|
192
|
0 |
0 |
$options->{'visibility'} =~ /pack/ ? : |
|
195
|
0 |
0 |
if $options->{'name'} |
|
197
|
0 |
0 |
if $options->{'description'} |
|
198
|
0 |
0 |
if (my $color = $options->{'color'}) |
|
201
|
0 |
0 |
if (my $color = $options->{'altColor'}) |
|
204
|
0 |
0 |
if (exists $options->{'viewLimits'} and my($low, $hi) = split(/:/, $options->{'viewLimits'}, 3)) |
|
208
|
0 |
0 |
if (exists $options->{'maxHeightPixels'} and my($max, $default, $min) = split(/:/, $options->{'maxHeightPixels'}, 4)) |
|
213
|
0 |
0 |
if $options->{'windowingFunction'} |
|
218
|
0 |
0 |
if $options->{'smoothingWindow'} |
|
233
|
0 |
1 |
unless $type =~ /^(gff3|featurefile)$/i |
|
239
|
1 |
0 |
if ($type eq 'gff3') { } |
|
252
|
1 |
0 |
if defined $name |
|
253
|
0 |
1 |
if defined $note |
|
259
|
0 |
1 |
unless $seqid |
|
262
|
1 |
0 |
if ($type eq 'gff3') { } |
|
298
|
0 |
1 |
if /^#/ |
|
299
|
0 |
1 |
unless /\S/ |
|
301
|
0 |
1 |
if (/^track/) |
|
306
|
0 |
1 |
if (/^fixedStep/) |
|
311
|
1 |
0 |
if (/^variableStep/) |
|
316
|
0 |
1 |
if (/^\S+\s+\d+\s+\d+\s+-?[\dEe.]+/) |
|
321
|
1 |
0 |
if ($format ne 'none') |
|
326
|
0 |
1 |
$format eq 'bed' ? : |
|
|
1 |
0 |
unless $self->{'track_options'}{'chrom'} and exists $self->current_track->{'seqids'}{$self->{'track_options'}{'chrom'}}{'min'} |
|
329
|
0 |
1 |
if $format eq 'bed' |
|
330
|
0 |
1 |
if $format eq 'fixed' |
|
331
|
1 |
0 |
if $format eq 'variable' |
|
336
|
0 |
1 |
if defined $_ and /^(track|variableStep|fixedStep)/ |
|
348
|
0 |
0 |
unless $options{'type'} eq 'wiggle_0' |
|
360
|
0 |
0 |
unless exists $options{'chrom'} |
|
361
|
0 |
0 |
unless exists $options{'start'} |
|
362
|
0 |
0 |
unless exists $options{'step'} |
|
372
|
0 |
1 |
unless exists $options{'chrom'} |
|
398
|
0 |
1 |
if ($self->allow_sampling and (my $size = &Bio::Graphics::Wiggle::Loader::stat($infh)->size) > 5000000) |
|
408
|
0 |
1 |
if ($bedline) |
|
412
|
0 |
0 |
if $transform |
|
418
|
0 |
3809 |
if /^track/ |
|
419
|
0 |
3809 |
if /chrom=(\S+)/ and $1 ne $chrom |
|
420
|
0 |
3809 |
if /^\#|fixedStep|variableStep/ |
|
421
|
0 |
3809 |
unless my @tokens = split(/\s+/, $_, 0) |
|
422
|
0 |
3809 |
@tokens > 3 ? : |
|
424
|
0 |
3809 |
if $transform |
|
449
|
0 |
0 |
unless seek $fh, int rand $size, 0 |
|
452
|
0 |
0 |
unless $line |
|
455
|
0 |
0 |
unless $value =~ /^[\d\seE.+-]+$/ |
|
456
|
0 |
0 |
if $transform |
|
472
|
0 |
2 |
if $transform |
|
481
|
0 |
0 |
if $value == 0 |
|
488
|
0 |
0 |
if $value == 0 |
|
489
|
0 |
0 |
if ($value < 0) { } |
|
501
|
0 |
0 |
if $oops |
|
503
|
0 |
0 |
if /^track/ |
|
504
|
0 |
0 |
if /^#/ |
|
515
|
0 |
0 |
if $transform |
|
524
|
0 |
0 |
unless exists $self->current_track->{'seqids'}{$seqid}{'start'} and $self->current_track->{'seqids'}{$seqid}{'start'} < $start |
|
528
|
0 |
0 |
unless exists $self->current_track->{'seqids'}{$seqid}{'end'} and $self->current_track->{'seqids'}{$seqid}{'end'} > $end |
|
544
|
0 |
0 |
if not defined $chrom->{'start'} or $chrom->{'start'} > $start |
|
547
|
0 |
0 |
if not defined $chrom->{'end'} or $chrom->{'end'} < $end |
|
554
|
0 |
0 |
if /^(track|variableStep|fixedStep)/ |
|
555
|
0 |
0 |
if /^#/ |
|
558
|
0 |
0 |
if (@buffer >= 500000) |
|
559
|
0 |
0 |
if $transform |
|
568
|
0 |
0 |
if $transform |
|
569
|
0 |
0 |
if @buffer |
|
584
|
0 |
3809 |
if /^(track|variableStep|fixedStep)/ |
|
585
|
0 |
3809 |
if /^#/ |
|
587
|
0 |
3809 |
unless my($start, $value) = split(/\s+/, $_, 3) |
|
588
|
0 |
3809 |
if $transform |
|
589
|
0 |
3809 |
unless eval {
do {
$wigfile->set_value($start, $value);
1
}
} |
|
596
|
1 |
3808 |
if not defined $chrom->{'start'} or $chrom->{'start'} > $start |
|
599
|
3809 |
0 |
if not defined $chrom->{'end'} or $chrom->{'end'} < $end |
|
613
|
1 |
0 |
unless (exists $self->current_track->{'seqids'}{$seqid}{'wig'}) |
|
629
|
0 |
1 |
unless ($class->can('new')) |
|
632
|
0 |
0 |
if $@ |
|
645
|
0 |
1 |
unless $wigfile |
|
654
|
0 |
0 |
unless $rgb =~ /\d+,\d+,\d+/ |
|
663
|
0 |
0 |
unless (%Bio::Graphics::Wiggle::Loader::color_name) |
|
666
|
0 |
0 |
unless my($hex, $name) = split(' ', $_, 3) |
|
676
|
0 |
1 |
unless @args |
|
680
|
0 |
1 |
unless defined $_ |