| line |
true |
false |
branch |
|
218
|
1 |
861 |
if $meta |
|
219
|
800 |
62 |
if $qual |
|
220
|
1 |
861 |
if $trace |
|
221
|
2 |
860 |
if $trace_indices |
|
253
|
1 |
713 |
if ref $value and ref $value ne 'ARRAY' and $value->isa('Bio::Seq::PrimaryQual') |
|
256
|
833 |
673 |
if $value |
|
491
|
0 |
0 |
unless (defined $self->{'trace_data'}) |
|
492
|
0 |
0 |
unless (grep {lc $trace eq $_;} 'a', 'g', 'c', 't') |
|
496
|
0 |
0 |
exists $self->{'trace_data'}{$trace} && ref $self->{'trace_data'}{$trace} eq 'ARRAY' ? : |
|
498
|
0 |
0 |
if (defined $scale and $scale != 0) |
|
521
|
310 |
916 |
if (defined $value) |
|
522
|
0 |
310 |
unless $value =~ /^[-+]?\d+$/ |
|
525
|
204 |
106 |
if defined $self->{'_threshold'} and $self->{'_threshold'} ne $value |
|
549
|
0 |
4 |
if defined $threshold |
|
552
|
4 |
0 |
unless defined $self->{'_ranges'} |
|
561
|
36 |
28 |
if $maskQual->[$i] < $self->{'_threshold'} |
|
588
|
0 |
301 |
if defined $threshold |
|
591
|
301 |
0 |
unless defined $self->{'_ranges'} |
|
615
|
0 |
300 |
if defined $threshold |
|
618
|
0 |
300 |
unless defined $self->{'_ranges'} |
|
645
|
2 |
301 |
if defined $threshold |
|
648
|
2 |
301 |
unless defined $self->{'_ranges'} |
|
651
|
0 |
303 |
unless defined $self->{'_ranges'} |
|
685
|
0 |
2 |
unless $minl =~ /^\+?\d+$/ |
|
689
|
0 |
2 |
unless defined $self->{'_ranges'} |
|
694
|
1 |
5 |
if $r->{'length'} < $minl |
|
715
|
0 |
307 |
unless defined $self->threshold |
|
724
|
209142 |
91048 |
if ($rangeFlag) { } |
|
726
|
58505 |
150637 |
if ($qual->[$i] < $threshold) |
|
740
|
58920 |
32128 |
if ($qual->[$i] >= $threshold) |
|
748
|
201 |
106 |
if ($rangeFlag) |