| line |
!l |
l&&!r |
l&&r |
condition |
|
1211
|
2 |
0 |
0 |
ref $args{'-type'} and ref $args{'-type'} eq 'ARRAY'
|
|
1245
|
2 |
0 |
0 |
exists $args{'-iterator'} and $args{'-iterator'}
|
|
1297
|
0 |
0 |
0 |
$f->start == $start and $f->end == $end
|
|
1319
|
3 |
0 |
0 |
ref $args{'-type'} and ref $args{'-type'} eq 'ARRAY'
|
|
1448
|
0 |
0 |
6 |
$chromo and $strand
|
|
|
0 |
0 |
6 |
$chromo and $strand and defined $start
|
|
|
0 |
0 |
6 |
$chromo and $strand and defined $start and defined $stop
|
|
|
0 |
0 |
6 |
$chromo and $strand and defined $start and defined $stop and $number
|
|
|
0 |
0 |
6 |
$chromo and $strand and defined $start and defined $stop and $number and $extension
|
|
2452
|
0 |
2 |
0 |
$iterator->strand == 0 and $useq->stranded
|
|
2559
|
0 |
0 |
1 |
$self->{'bin'} and $step > 1
|
|
2707
|
0 |
0 |
0 |
$bins and $bins > 1
|
| line |
l |
!l |
condition |
|
900
|
0 |
0 |
$args{'-file'} || $args{'-useq'} || undef
|
|
1097
|
0 |
0 |
$sum || 0
|
|
|
0 |
0 |
$sum_squares || 0
|
|
|
0 |
0 |
$min || 0
|
|
|
0 |
0 |
$max || 0
|
|
1210
|
0 |
0 |
$args{'-types'} || $args{'-primary_tag'} || 'region'
|
|
1212
|
0 |
0 |
$args{'-type'}[0] || 'region'
|
|
1288
|
0 |
0 |
$type || undef
|
|
1318
|
0 |
1 |
$args{'-types'} || $args{'-primary_tag'} || 'region'
|
|
1320
|
0 |
0 |
$args{'-type'}[0] || 'region'
|
|
1508
|
0 |
0 |
$args{'-seq_id'} || $args{'-chromo'} || undef
|
|
1509
|
0 |
0 |
$args{'-start'} || $args{'-pos'} || undef
|
|
1510
|
0 |
0 |
$args{'-end'} || $args{'-stop'} || undef
|
|
1511
|
0 |
5 |
$args{'-strand'} || '0'
|
|
1520
|
5 |
0 |
$start ||= 1
|
|
1522
|
0 |
5 |
$strand ||= 0
|
|
2142
|
1407 |
869 |
$r->[2] || 0
|
|
2184
|
11 |
0 |
$sum || 0
|
|
|
11 |
0 |
$sum_squares || 0
|
|
|
0 |
11 |
$min || 0
|
|
|
11 |
0 |
$max || 0
|
|
2337
|
0 |
0 |
$type ||= 'region'
|
|
2350
|
0 |
1 |
$type ||= 'region'
|
|
2387
|
0 |
0 |
$bins ||= 1
|
|
2509
|
2 |
0 |
shift @{$$self{'slices'};} || undef
|
|
2618
|
0 |
1 |
$useq->slice_strand($slices->[0]) || 0
|
|
2643
|
0 |
1 |
$self->{'useq'}->slice_strand($slices->[0]) || 0
|
|
2727
|
0 |
0 |
$sum || 0
|
|
|
0 |
0 |
$sum_squares || 0
|
|
|
0 |
0 |
$min || 0
|
|
|
0 |
0 |
$max || 0
|
|
2776
|
1 |
0 |
$bin ||= 1
|
| line |
l |
!l&&r |
!l&&!r |
condition |
|
1092
|
0 |
0 |
0 |
not defined $min or $stats->{'minVal'} < $min
|
|
1093
|
0 |
0 |
0 |
not defined $max or $stats->{'maxVal'} < $max
|
|
1210
|
2 |
0 |
0 |
$args{'-type'} ||= $args{'-types'} || $args{'-primary_tag'} || 'region'
|
|
1318
|
2 |
1 |
0 |
$args{'-type'} ||= $args{'-types'} || $args{'-primary_tag'} || 'region'
|
|
1485
|
2 |
4 |
0 |
$self->{'coord2file'}{$chromo}{$strand} ||= 'Set::IntervalTree'->new
|
|
1521
|
5 |
0 |
0 |
$stop ||= $self->length($seq_id)
|
|
2177
|
11 |
33 |
21101 |
not defined $min or $r->[2] < $min
|
|
2178
|
11 |
133 |
21001 |
not defined $max or $r->[2] > $max
|
|
2373
|
0 |
0 |
0 |
$bins ||= $self->length
|
|
2380
|
0 |
0 |
0 |
$bins ||= $self->length
|
|
2722
|
0 |
0 |
0 |
not defined $min or $s < $min
|
|
2723
|
0 |
0 |
0 |
not defined $max or $s > $max
|
|
2775
|
1 |
0 |
0 |
$bin ||= $self->{'bin'}
|
|
2778
|
0 |
1 |
0 |
$step ||= $self->length / $bin
|