| line |
true |
false |
branch |
|
210
|
0 |
20 |
if ($self->seqid_weight eq "count" and not defined $self->expression_matrix)
|
|
216
|
0 |
20 |
if ($self->count_loops_by eq 'coverage' and not defined $self->coverage) { }
|
|
|
0 |
40 |
elsif ($self->count_loops_by eq 'number_of_reads' and not defined $self->number_of_reads) { }
|
|
234
|
0 |
20 |
if ($self->strand_bias eq 'plus') { }
|
|
|
0 |
20 |
elsif ($self->strand_bias eq 'minus') { }
|
|
|
20 |
0 |
elsif ($self->strand_bias eq 'random') { }
|
|
264
|
0 |
860 |
if /^;/u
|
|
265
|
100 |
760 |
if (/^>/u) { }
|
|
281
|
0 |
100 |
if (defined $fields[1])
|
|
287
|
0 |
760 |
unless defined $id
|
|
297
|
0 |
20 |
unless (%indexed_fasta)
|
|
302
|
0 |
20 |
unless $fh->close
|
|
304
|
0 |
20 |
if %fasta_rtree
|
|
320
|
20 |
0 |
unless ($self->truncate)
|
|
325
|
50 |
50 |
if ($class eq 'App::Sandy::Seq::SingleEnd') { }
|
|
|
50 |
0 |
elsif ($class eq 'App::Sandy::Seq::PairedEnd') { }
|
|
327
|
0 |
50 |
if ($index_size < $read_mean)
|
|
334
|
0 |
50 |
if ($index_size < $fragment_mean)
|
|
345
|
0 |
20 |
unless (%$indexed_fasta)
|
|
350
|
0 |
20 |
unless ($self->_has_no_fasta_rtree)
|
|
352
|
0 |
0 |
if @blacklist
|
|
362
|
0 |
20 |
unless ($self->_has_no_fasta_rtree)
|
|
399
|
0 |
0 |
unless ($init)
|
|
405
|
0 |
0 |
if ($en < $pos - 1)
|
|
415
|
0 |
100 |
if ($init)
|
|
420
|
50 |
50 |
$class eq 'App::Sandy::Seq::SingleEnd' ? :
|
|
424
|
0 |
100 |
if ($len > $seq_len - $read_len) { }
|
|
433
|
0 |
20 |
unless (%$indexed_fasta)
|
|
438
|
0 |
20 |
unless ($self->_has_no_fasta_rtree)
|
|
440
|
0 |
0 |
if @blacklist_id
|
|
461
|
0 |
20 |
if ($self->seqid_weight eq 'same') { }
|
|
|
0 |
20 |
elsif ($self->seqid_weight eq 'count') { }
|
|
|
20 |
0 |
elsif ($self->seqid_weight eq 'length') { }
|
|
469
|
0 |
0 |
if ($weights->[$i] > 1)
|
|
487
|
0 |
0 |
unless (exists $piece_table->{$id} or $self->_exists_fasta_tree($id))
|
|
494
|
0 |
0 |
unless (%$indexed_file)
|
|
505
|
0 |
0 |
if (exists $piece_table->{$seq_id}) { }
|
|
512
|
0 |
0 |
unless (@$ids)
|
|
539
|
0 |
0 |
if (%ptable_ind)
|
|
590
|
0 |
0 |
unless (@$keys and @$weights)
|
|
638
|
0 |
20 |
if ($min <= 0)
|
|
642
|
0 |
20 |
$min < 1 ? :
|
|
666
|
100 |
0 |
scalar keys %$type_h == 1 ? :
|
|
689
|
0 |
20 |
if ($self->genomic_variation)
|
|
707
|
0 |
20 |
if (defined $genomic_variation)
|
|
730
|
0 |
100 |
if (defined $indexed_snv and defined $indexed_snv->{$std_seq_id})
|
|
736
|
0 |
0 |
if (@snvs_homo)
|
|
767
|
100 |
0 |
unless ($self->truncate)
|
|
770
|
50 |
50 |
if ($class eq 'App::Sandy::Seq::SingleEnd') { }
|
|
|
50 |
0 |
elsif ($class eq 'App::Sandy::Seq::PairedEnd') { }
|
|
771
|
0 |
50 |
if ($new_size < $self->seq->read_mean)
|
|
776
|
0 |
50 |
if ($new_size < $self->seq->fragment_mean)
|
|
792
|
100 |
0 |
if (%$type_h) { }
|
|
801
|
0 |
20 |
unless (%piece_table)
|
|
807
|
0 |
20 |
unless ($self->_has_no_fasta_rtree)
|
|
809
|
0 |
0 |
if @blacklist
|
|
828
|
0 |
0 |
defined $snv->{'id'} && $snv->{'id'} ne '.' ? :
|
|
831
|
0 |
0 |
if ($snv->{'ref'} eq '-') { }
|
|
|
0 |
0 |
elsif ($snv->{'alt'} eq '-') { }
|
|
855
|
0 |
0 |
unless (defined $seq_id and exists $indexed_fasta->{$seq_id})
|
|
867
|
0 |
0 |
if ($snv->{'ref'} eq '-' and $snv->{'pos'} > $size or $snv->{'ref'} ne '-' and $snv->{'pos'} >= $size) { }
|
|
|
0 |
0 |
elsif ($snv->{'ref'} ne '-') { }
|
|
877
|
0 |
0 |
if (uc $ref ne uc $snv->{'ref'})
|
|
889
|
0 |
0 |
if (@saved_snvs)
|
|
899
|
8 |
0 |
if ($self->count_loops_by eq 'coverage') { }
|
|
|
0 |
0 |
elsif ($self->count_loops_by eq 'number-of-reads') { }
|
|
907
|
3 |
5 |
if ref $self->seq eq "App::Sandy::Seq::PairedEnd"
|
|
917
|
0 |
8 |
if ($number_of_reads <= 0)
|
|
927
|
0 |
0 |
if $self->_has_no_fasta_rtree
|
|
933
|
0 |
0 |
if defined $pid
|
|
1000
|
0 |
8 |
if ($output_format =~ /(sam|bam)/u) { }
|
|
|
8 |
0 |
elsif ($output_format =~ /fastq/u) { }
|
|
1003
|
5 |
3 |
if ($seq_class eq 'App::Sandy::Seq::SingleEnd') { }
|
|
|
3 |
0 |
elsif ($seq_class eq 'App::Sandy::Seq::PairedEnd') { }
|
|
1007
|
0 |
3 |
if $self->join_paired_ends
|
|
1011
|
0 |
8 |
if ($output_format eq "fastq.gz")
|
|
1050
|
0 |
8 |
$number_of_jobs == 1 ? :
|
|
1060
|
10 |
4 |
if my $pid = $pm->start
|
|
1081
|
2 |
2 |
if $tid == $number_of_jobs
|
|
1093
|
4 |
0 |
if ($output_format =~ /^(sam|fastq)$/u) { }
|
|
|
0 |
0 |
elsif ($output_format eq 'fastq.gz') { }
|
|
|
0 |
0 |
elsif ($output_format eq 'bam') { }
|
|
1107
|
0 |
4 |
if ($seq_class eq "App::Sandy::Seq::PairedEnd" and $file_class =~ /(sam|bam|join)/u)
|
|
1117
|
0 |
4 |
if ($output_format =~ /^(sam|bam)$/u and $tid == 1)
|
|
1134
|
6840 |
0 |
unless (@_)
|
|
1155
|
0 |
4 |
if ($output_format eq "bam" and $tid == $number_of_jobs)
|
|
1169
|
0 |
4 |
if ($sig->signal_catched)
|
|
1182
|
0 |
5 |
unless rename $tmp, $file
|
|
1193
|
0 |
5 |
unless &cat($tmp_files[$i], $fh[$fh_idx])
|
|
1197
|
0 |
5 |
unless unlink $tmp_files[$i]
|
|
1204
|
0 |
5 |
unless close $fh[$fh_idx]
|
|
1208
|
0 |
4 |
if ($self->count_loops_by eq 'number-of-reads') { }
|
|
1211
|
0 |
0 |
ref $self->seq eq 'App::Sandy::Seq::PairedEnd' ? :
|
|
1227
|
0 |
0 |
unless close $fh
|
|
1233
|
0 |
0 |
if (%$parent_count)
|
|
1246
|
0 |
0 |
unless close $fh
|
|
1261
|
0 |
4 |
unless close $fh
|