| 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) |
|
326
|
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 $size = &Bio::Graphics::Wiggle::Loader::stat($infh)->size) > 5000000 |
|
419
|
3809 |
0 |
0 |
/chrom=(\S+)/ and $1 ne $chrom |
|
524
|
0 |
0 |
0 |
exists $self->current_track->{'seqids'}{$seqid}{'start'} and $self->current_track->{'seqids'}{$seqid}{'start'} < $start |
|
528
|
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' |
|
618
|
0 |
0 |
$self->current_track->{'seqids'}{$seqid}{$_} || $self->{'FILEWIDE_STATS'}{$_} || (next) |
|
622
|
0 |
1 |
$self->{'track_options'}{'step'} || 1 |
|
625
|
0 |
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 |
|
544
|
0 |
0 |
0 |
not defined $chrom->{'start'} or $chrom->{'start'} > $start |
|
547
|
0 |
0 |
0 |
not defined $chrom->{'end'} or $chrom->{'end'} < $end |
|
596
|
1 |
0 |
3808 |
not defined $chrom->{'start'} or $chrom->{'start'} > $start |
|
599
|
1 |
3808 |
0 |
not defined $chrom->{'end'} or $chrom->{'end'} < $end |
|
604
|
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 |