| line |
!l |
l&&!r |
l&&r |
condition |
|
202
|
20 |
0 |
0 |
$self->seqid_weight eq 'count' and not defined $self->expression_matrix
|
|
208
|
0 |
20 |
0 |
$self->count_loops_by eq 'coverage' and not defined $self->coverage
|
|
|
20 |
0 |
0 |
$self->count_loops_by eq 'number_of_reads' and not defined $self->number_of_reads
|
|
509
|
0 |
0 |
0 |
@$keys and @$weights
|
|
647
|
100 |
0 |
0 |
defined $indexed_snv and defined $indexed_snv->{$std_seq_id}
|
|
745
|
0 |
0 |
0 |
defined $snv->{'id'} && $snv->{'id'} ne '.'
|
|
772
|
0 |
0 |
0 |
defined $seq_id and exists $indexed_fasta->{$seq_id}
|
|
784
|
0 |
0 |
0 |
$snv->{'ref'} eq '-' and $snv->{'pos'} > $size
|
|
|
0 |
0 |
0 |
$snv->{'ref'} ne '-' and $snv->{'pos'} >= $size
|
|
1027
|
2 |
2 |
0 |
$seq_class eq 'App::Sandy::Seq::PairedEnd' and $file_class =~ /(sam|bam|join)/u
|
|
1037
|
4 |
0 |
0 |
$output_format =~ /^(sam|bam)$/u and $tid == 1
|
|
1043
|
4 |
0 |
1710 |
$i <= $last_read_idx and not $sig->signal_catched
|
|
1074
|
4 |
0 |
0 |
$output_format eq 'bam' and $tid == $number_of_jobs
|
|
1134
|
4 |
0 |
0 |
$self->count_loops_by eq 'number-of-reads' and ref $self->seq eq 'App::Sandy::Seq::PairedEnd'
|