| line |
true |
false |
branch |
|
202
|
0 |
20 |
if ($self->seqid_weight eq 'count' and not defined $self->expression_matrix)
|
|
208
|
0 |
20 |
if ($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 $self->number_of_reads) { }
|
|
225
|
0 |
20 |
if ($self->strand_bias eq 'plus') { }
|
|
|
0 |
20 |
elsif ($self->strand_bias eq 'minus') { }
|
|
|
20 |
0 |
elsif ($self->strand_bias eq 'random') { }
|
|
254
|
0 |
860 |
if /^;/u
|
|
255
|
100 |
760 |
if (/^>/u) { }
|
|
271
|
0 |
100 |
if (defined $fields[1])
|
|
277
|
0 |
760 |
unless defined $id
|
|
287
|
0 |
20 |
unless (%indexed_fasta)
|
|
292
|
0 |
20 |
unless $fh->close
|
|
294
|
0 |
20 |
if %fasta_rtree
|
|
310
|
20 |
0 |
unless ($self->truncate)
|
|
315
|
50 |
50 |
if ($class eq 'App::Sandy::Seq::SingleEnd') { }
|
|
|
50 |
0 |
elsif ($class eq 'App::Sandy::Seq::PairedEnd') { }
|
|
317
|
0 |
50 |
if ($index_size < $read_mean)
|
|
324
|
0 |
50 |
if ($index_size < $fragment_mean)
|
|
335
|
0 |
20 |
unless (%$indexed_fasta)
|
|
340
|
0 |
20 |
unless ($self->_has_no_fasta_rtree)
|
|
342
|
0 |
0 |
if @blacklist
|
|
352
|
0 |
20 |
unless ($self->_has_no_fasta_rtree)
|
|
381
|
0 |
20 |
if ($self->seqid_weight eq 'same') { }
|
|
|
0 |
20 |
elsif ($self->seqid_weight eq 'count') { }
|
|
|
20 |
0 |
elsif ($self->seqid_weight eq 'length') { }
|
|
389
|
0 |
0 |
if ($weights->[$i] > 1)
|
|
406
|
0 |
0 |
unless (exists $piece_table->{$id} or $self->_exists_fasta_tree($id))
|
|
413
|
0 |
0 |
unless (%$indexed_file)
|
|
424
|
0 |
0 |
if (exists $piece_table->{$seq_id}) { }
|
|
431
|
0 |
0 |
unless (@$ids)
|
|
458
|
0 |
0 |
if (%ptable_ind)
|
|
509
|
0 |
0 |
unless (@$keys and @$weights)
|
|
555
|
0 |
20 |
if ($min <= 0)
|
|
559
|
0 |
20 |
$min < 1 ? :
|
|
583
|
100 |
0 |
scalar keys %$type_h == 1 ? :
|
|
606
|
0 |
20 |
if ($self->genomic_variation)
|
|
624
|
0 |
20 |
if (defined $genomic_variation)
|
|
647
|
0 |
100 |
if (defined $indexed_snv and defined $indexed_snv->{$std_seq_id})
|
|
653
|
0 |
0 |
if (@snvs_homo)
|
|
684
|
100 |
0 |
unless ($self->truncate)
|
|
687
|
50 |
50 |
if ($class eq 'App::Sandy::Seq::SingleEnd') { }
|
|
|
50 |
0 |
elsif ($class eq 'App::Sandy::Seq::PairedEnd') { }
|
|
688
|
0 |
50 |
if ($new_size < $self->seq->read_mean)
|
|
693
|
0 |
50 |
if ($new_size < $self->seq->fragment_mean)
|
|
709
|
100 |
0 |
if (%$type_h) { }
|
|
718
|
0 |
20 |
unless (%piece_table)
|
|
724
|
0 |
20 |
unless ($self->_has_no_fasta_rtree)
|
|
726
|
0 |
0 |
if @blacklist
|
|
745
|
0 |
0 |
defined $snv->{'id'} && $snv->{'id'} ne '.' ? :
|
|
748
|
0 |
0 |
if ($snv->{'ref'} eq '-') { }
|
|
|
0 |
0 |
elsif ($snv->{'alt'} eq '-') { }
|
|
772
|
0 |
0 |
unless (defined $seq_id and exists $indexed_fasta->{$seq_id})
|
|
784
|
0 |
0 |
if ($snv->{'ref'} eq '-' and $snv->{'pos'} > $size or $snv->{'ref'} ne '-' and $snv->{'pos'} >= $size) { }
|
|
|
0 |
0 |
elsif ($snv->{'ref'} ne '-') { }
|
|
794
|
0 |
0 |
if (uc $ref ne uc $snv->{'ref'})
|
|
806
|
0 |
0 |
if (@saved_snvs)
|
|
816
|
8 |
0 |
if ($self->count_loops_by eq 'coverage') { }
|
|
|
0 |
0 |
elsif ($self->count_loops_by eq 'number-of-reads') { }
|
|
824
|
3 |
5 |
if ref $self->seq eq 'App::Sandy::Seq::PairedEnd'
|
|
834
|
0 |
8 |
if ($number_of_reads <= 0)
|
|
844
|
4 |
0 |
defined $inc ? :
|
|
852
|
4 |
0 |
if $self->_has_no_fasta_rtree
|
|
858
|
0 |
0 |
if defined $pid
|
|
881
|
0 |
8 |
$simulation eq 'transcriptome' ? :
|
|
923
|
0 |
8 |
if ($output_format =~ /(sam|bam)/u) { }
|
|
|
8 |
0 |
elsif ($output_format =~ /fastq/u) { }
|
|
926
|
5 |
3 |
if ($seq_class eq 'App::Sandy::Seq::SingleEnd') { }
|
|
|
3 |
0 |
elsif ($seq_class eq 'App::Sandy::Seq::PairedEnd') { }
|
|
930
|
0 |
3 |
if $self->join_paired_ends
|
|
934
|
0 |
8 |
if ($output_format eq 'fastq.gz')
|
|
973
|
0 |
8 |
$number_of_jobs == 1 ? :
|
|
983
|
10 |
4 |
if my $pid = $pm->start
|
|
1001
|
2 |
2 |
if $tid == $number_of_jobs
|
|
1013
|
4 |
0 |
if ($output_format =~ /^(sam|fastq)$/u) { }
|
|
|
0 |
0 |
elsif ($output_format eq 'fastq.gz') { }
|
|
|
0 |
0 |
elsif ($output_format eq 'bam') { }
|
|
1027
|
0 |
4 |
if ($seq_class eq 'App::Sandy::Seq::PairedEnd' and $file_class =~ /(sam|bam|join)/u)
|
|
1037
|
0 |
4 |
if ($output_format =~ /^(sam|bam)$/u and $tid == 1)
|
|
1053
|
1710 |
0 |
unless (@_)
|
|
1074
|
0 |
4 |
if ($output_format eq 'bam' and $tid == $number_of_jobs)
|
|
1088
|
0 |
4 |
if ($sig->signal_catched)
|
|
1101
|
0 |
5 |
unless rename $tmp, $file
|
|
1112
|
0 |
5 |
unless &cat($tmp_files[$i], $fh[$fh_idx])
|
|
1116
|
0 |
5 |
unless unlink $tmp_files[$i]
|
|
1123
|
0 |
5 |
unless close $fh[$fh_idx]
|
|
1134
|
0 |
4 |
if ($self->count_loops_by eq 'number-of-reads' and ref $self->seq eq 'App::Sandy::Seq::PairedEnd')
|
|
1155
|
0 |
4 |
unless close $count_fh
|