| line |
!l |
l&&!r |
l&&r |
condition |
|
137
|
0 |
0 |
1 |
-d $base and -w _
|
|
204
|
0 |
0 |
0 |
exists $$options{'viewLimits'} and my($low, $hi) = split(/:/, $$options{'viewLimits'}, 3)
|
|
208
|
0 |
0 |
0 |
exists $$options{'maxHeightPixels'} and my($max, $default, $min) = split(/:/, $$options{'maxHeightPixels'}, 4)
|
|
324
|
0 |
1 |
0 |
$$self{'track_options'}{'chrom'} and exists $self->current_track->{'seqids'}{$$self{'track_options'}{'chrom'}}{'min'}
|
|
336
|
1 |
0 |
0 |
defined $_ and /^(track|variableStep|fixedStep)/
|
|
398
|
1 |
0 |
0 |
$self->allow_sampling and (my $size = stat($infh)->size) > 5000000
|
|
419
|
3809 |
0 |
0 |
/chrom=(\S+)/ and $1 ne $chrom
|
|
522
|
0 |
0 |
0 |
exists $self->current_track->{'seqids'}{$seqid}{'start'} and $self->current_track->{'seqids'}{$seqid}{'start'} < $start
|
|
526
|
0 |
0 |
0 |
exists $self->current_track->{'seqids'}{$seqid}{'end'} and $self->current_track->{'seqids'}{$seqid}{'end'} > $end
|
| line |
l |
!l |
condition |
|
135
|
1 |
0 |
shift() || 'track'
|
|
136
|
0 |
1 |
shift() || 'Bio::Graphics::Wiggle'
|
|
165
|
0 |
0 |
$method ||= 'microarray_oligo'
|
|
166
|
0 |
0 |
$source ||= '.'
|
|
175
|
0 |
0 |
$$options{'visibility'} ||= 'dense'
|
|
215
|
0 |
0 |
$$options{'smoothingWindow'} || 0
|
|
229
|
0 |
1 |
$method ||= 'microarray_oligo'
|
|
230
|
0 |
1 |
$source ||= '.'
|
|
232
|
1 |
0 |
$type ||= 'featurefile'
|
|
385
|
15 |
1 |
$$self{'tracks'}{$$self{'tracknum'}} ||= {}
|
|
395
|
1 |
0 |
$self->current_track->{'seqids'} ||= {}
|
|
541
|
0 |
0 |
$wigfile->span || 1
|
|
612
|
1 |
0 |
$$self{'trackname'} || 'track'
|
|
617
|
4 |
0 |
$self->current_track->{'seqids'}{$seqid}{$_} || $$self{'FILEWIDE_STATS'}{$_} || (next)
|
|
622
|
0 |
1 |
$$self{'track_options'}{'step'} || 1
|
|
623
|
1 |
0 |
$$self{'track_options'}{'span'} || $$self{'track_options'}{'step'} || 1
|
|
626
|
0 |
1 |
$self->current_track->{'display_options'}{'trim'} || 'stdev10'
|
| line |
l |
!l&&r |
!l&&!r |
condition |
|
138
|
0 |
1 |
0 |
ref $class || $class
|
|
173
|
0 |
0 |
0 |
$$options{'name'} ||= $track
|
|
176
|
0 |
0 |
0 |
$$options{'color'} ||= $$options{'visibility'} =~ /pack/i ? '255,0,0' : '0,0,0'
|
|
177
|
0 |
0 |
0 |
$$options{'altColor'} ||= $$options{'visibility'} =~ /pack/i ? '0,0,255' : '0,0,0'
|
|
248
|
0 |
1 |
0 |
$$options{'name'} ||= $track
|
|
400
|
0 |
0 |
0 |
$$self{'FILEWIDE_STATS'} ||= $self->sample_file($infh, 5000)
|
|
413
|
0 |
0 |
0 |
$stats{$seqid} ||= 'Statistics::Descriptive::Sparse'->new
|
|
425
|
3808 |
1 |
0 |
$stats{$seqid} ||= 'Statistics::Descriptive::Sparse'->new
|
|
541
|
0 |
0 |
0 |
$$self{'track_options'}{'span'} ||= $wigfile->span || 1
|
|
543
|
0 |
0 |
0 |
not defined $$chrom{'start'} or $$chrom{'start'} > $start
|
|
546
|
0 |
0 |
0 |
not defined $$chrom{'end'} or $$chrom{'end'} < $end
|
|
595
|
1 |
0 |
3808 |
not defined $$chrom{'start'} or $$chrom{'start'} > $start
|
|
598
|
1 |
3808 |
0 |
not defined $$chrom{'end'} or $$chrom{'end'} < $end
|
|
603
|
1 |
0 |
0 |
$self->current_track->{'seqids'}{$seqid}{'end'} ||= $self->current_track->{'seqids'}{$seqid}{'start'}
|
|
670
|
0 |
0 |
0 |
$Bio::Graphics::Wiggle::Loader::color_name{$clr} || $clr
|