| line |
!l |
l&&!r |
l&&r |
condition |
|
210
|
20 |
0 |
0 |
$self->seqid_weight eq "count" and not defined $self->expression_matrix
|
|
216
|
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 $self->number_of_reads
|
|
590
|
0 |
0 |
0 |
@$keys and @$weights
|
|
730
|
100 |
0 |
0 |
defined $indexed_snv and defined $indexed_snv->{$std_seq_id}
|
|
828
|
0 |
0 |
0 |
defined $snv->{'id'} && $snv->{'id'} ne '.'
|
|
855
|
0 |
0 |
0 |
defined $seq_id and exists $indexed_fasta->{$seq_id}
|
|
867
|
0 |
0 |
0 |
$snv->{'ref'} eq "-" and $snv->{'pos'} > $size
|
|
|
0 |
0 |
0 |
$snv->{'ref'} ne "-" and $snv->{'pos'} >= $size
|
|
1107
|
2 |
2 |
0 |
$seq_class eq "App::Sandy::Seq::PairedEnd" and $file_class =~ /(sam|bam|join)/u
|
|
1117
|
4 |
0 |
0 |
$output_format =~ /^(sam|bam)$/u and $tid == 1
|
|
1123
|
4 |
0 |
6840 |
$i <= $last_read_idx and not $sig->signal_catched
|
|
1155
|
4 |
0 |
0 |
$output_format eq "bam" and $tid == $number_of_jobs
|