| line |
true |
false |
branch |
|
331
|
12 |
8 |
if (@_) |
|
332
|
0 |
12 |
if (scalar @_ == 1) { } |
|
339
|
12 |
0 |
if (exists $options{'file'} or $options{'table'}) |
|
343
|
4 |
8 |
if (exists $options{'do_exon'}) |
|
346
|
0 |
12 |
if (exists $options{'do_cds'}) |
|
349
|
0 |
12 |
if (exists $options{'do_utr'}) |
|
352
|
0 |
12 |
if (exists $options{'do_codon'}) |
|
355
|
0 |
12 |
if (exists $options{'source'}) |
|
358
|
8 |
4 |
if (exists $options{'class'}) |
|
360
|
8 |
0 |
if (eval "require $class; 1") { } |
|
380
|
20 |
86 |
if (@_) |
|
399
|
8 |
90 |
if (@_) |
|
408
|
0 |
62 |
if (@_) |
|
417
|
0 |
58 |
if (@_) |
|
426
|
0 |
62 |
if (@_) |
|
450
|
0 |
20 |
if ($self->{'stream'}) |
|
456
|
0 |
20 |
unless ($filename) |
|
464
|
0 |
20 |
unless my $Stream = "Bio::ToolBox::Data::Stream"->new("in", $filename) |
|
467
|
0 |
20 |
unless ($bed) |
|
473
|
4 |
16 |
$Stream->extension =~ /peak/i ? : |
|
474
|
0 |
20 |
$bed == 4 && $Stream->extension =~ /bdg|bedgraph/i ? : |
|
480
|
4 |
4 |
if ($c =~ /^track.+type=gappedpeak/i) { } |
|
|
0 |
4 |
elsif ($c =~ /^track.+type=narrowpeak/i) { } |
|
|
0 |
4 |
elsif ($c =~ /^track.+type=broadpeak/i) { } |
|
|
0 |
4 |
elsif ($c =~ /^track.+type=bedgraph/i) { } |
|
|
0 |
4 |
elsif ($c =~ /^track.+type=bed\s/i) { } |
|
|
0 |
4 |
elsif ($c =~ /^track.+type=(\w+)\s/i) { } |
|
509
|
4 |
16 |
if ($peak == 15) { } |
|
|
4 |
12 |
elsif ($peak == 10) { } |
|
|
0 |
12 |
elsif ($peak == 9) { } |
|
|
0 |
12 |
elsif ($bdg) { } |
|
|
6 |
6 |
elsif ($bed > 6) { } |
|
572
|
0 |
8 |
unless $self->{'stream'} |
|
574
|
2 |
6 |
if ($self->version eq 'bed12') { } |
|
588
|
0 |
138 |
unless ($self->fh) |
|
595
|
0 |
124 |
if ($line =~ /^#/ or $line =~ /^(?:track|browser)/ or not $line =~ /\w+/) |
|
601
|
0 |
124 |
unless ($feature) |
|
619
|
0 |
36 |
unless ($self->fh) |
|
622
|
0 |
36 |
unless ($self->{'eof'}) |
|
623
|
0 |
0 |
unless $self->parse_file |
|
630
|
6 |
0 |
unless ($self->{'eof'}) |
|
634
|
6 |
0 |
wantarray ? : |
|
642
|
0 |
14 |
unless ($self->fh) |
|
645
|
0 |
14 |
if $self->{'eof'} |
|
657
|
18 |
100 |
unless (exists $self->{'seq_ids'}{$s}) |
|
660
|
56 |
62 |
if $feature->end > $self->{'seq_ids'}{$s} |
|
669
|
0 |
16 |
unless (scalar @data == 10) |
|
699
|
0 |
0 |
unless (scalar @data == 9) |
|
728
|
0 |
0 |
unless (scalar @data == 9) |
|
748
|
0 |
22 |
unless (scalar @data == $self->{'bed'}) |
|
770
|
0 |
70 |
unless (scalar @data == $self->{'bed'}) |
|
828
|
0 |
16 |
unless (scalar @data == 15) |
|
878
|
0 |
0 |
unless (scalar keys %{$$self{"seq_ids"};}) |
|
882
|
0 |
0 |
wantarray ? : |
|
888
|
0 |
0 |
unless (scalar keys %{$$self{"seq_ids"};}) |
|
896
|
0 |
0 |
unless $self->{'eof'} |
|
899
|
0 |
0 |
unless (exists $self->{'seq_ids'}{$s}) |
|
902
|
0 |
0 |
if $_->end > $self->{'seq_ids'}{$s} |
|
908
|
0 |
0 |
unless $self->{'stream'} |
|
918
|
10 |
28 |
unless (exists $self->{'id2seqf'}) |
|
919
|
0 |
10 |
unless $self->{'eof'} |
|
923
|
0 |
86 |
if (exists $self->{'id2seqf'}{$name}) { } |
|
934
|
0 |
38 |
if (scalar @_ == 0) { } |
|
|
6 |
32 |
elsif (scalar @_ == 1) { } |
|
950
|
0 |
38 |
unless ($name) |
|
956
|
38 |
0 |
if (exists $self->{'id2seqf'}{lc $name}) |
|
964
|
32 |
6 |
if ($id) |
|
966
|
32 |
0 |
if ($g->primary_id eq $id) |
|
972
|
0 |
0 |
if ($chrom and $start and $end) |
|
974
|
0 |
0 |
if ($g->strand == $strand and not $g->start > $end || $g->end < $start) |
|
988
|
6 |
0 |
if (scalar @$genes == 1) { } |
|
|
0 |
0 |
elsif (scalar @$genes > 1) { } |