| 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 = $$options{'glyph'}) { }
|
|
182
|
0 |
0 |
if ($graph_type =~ /box/) { }
|
|
186
|
0 |
0 |
$graph_type =~ /density/ ? :
|
|
191
|
0 |
0 |
$$options{'visibility'} =~ /pack/ ? :
|
|
194
|
0 |
0 |
if $$options{'name'}
|
|
196
|
0 |
0 |
if $$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))
|
|
212
|
0 |
0 |
if $$options{'windowingFunction'}
|
|
217
|
0 |
0 |
if $$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')
|
|
324
|
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 $size = stat($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
|
|
522
|
0 |
0 |
unless exists $self->current_track->{'seqids'}{$seqid}{'start'} and $self->current_track->{'seqids'}{$seqid}{'start'} < $start
|
|
526
|
0 |
0 |
unless exists $self->current_track->{'seqids'}{$seqid}{'end'} and $self->current_track->{'seqids'}{$seqid}{'end'} > $end
|
|
543
|
0 |
0 |
if not defined $$chrom{'start'} or $$chrom{'start'} > $start
|
|
546
|
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
}
}
|
|
595
|
1 |
3808 |
if not defined $$chrom{'start'} or $$chrom{'start'} > $start
|
|
598
|
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 $_
|