| line |
true |
false |
branch |
|
446
|
723 |
935 |
if (ref $class) |
|
459
|
1658 |
0 |
if exists $args{'-strand'} |
|
464
|
0 |
1658 |
if (defined $self->[1] and defined $self->[2] and $self->[1] > $self->[2]) |
|
474
|
1658 |
0 |
if (defined $args{'-type'}) |
|
478
|
1638 |
20 |
if (defined $args{'-source'}) |
|
481
|
32 |
1626 |
if (exists $args{'-score'}) |
|
484
|
240 |
1418 |
if (exists $args{'-phase'}) |
|
487
|
1 |
1657 |
if (exists $args{'-attributes'} or exists $args{'-tags'}) |
|
489
|
1 |
0 |
if (ref $args{'-attributes'} eq "HASH") |
|
493
|
2 |
1656 |
if (exists $args{'-segments'}) |
|
496
|
0 |
16 |
unless (ref $s eq $class) |
|
509
|
0 |
1671 |
if (@_) |
|
512
|
1671 |
0 |
defined $self->[0] ? : |
|
517
|
0 |
6484 |
if (@_) |
|
520
|
6484 |
0 |
defined $self->[1] ? : |
|
525
|
9 |
2353 |
if (@_) |
|
528
|
2362 |
0 |
defined $self->[2] ? : |
|
533
|
1699 |
2545 |
if (@_) |
|
535
|
262 |
1437 |
if ($str eq '+') { } |
|
|
116 |
1321 |
elsif ($str eq '-') { } |
|
|
16 |
1305 |
elsif ($str eq '.') { } |
|
|
1207 |
98 |
elsif ($str =~ /^[\+\-]?1$/) { } |
|
|
98 |
0 |
elsif ($str eq '0') { } |
|
551
|
4244 |
0 |
defined $self->[3] ? : |
|
556
|
223 |
1966 |
if (@_) |
|
559
|
1900 |
289 |
defined $self->[4] ? : |
|
564
|
235 |
1776 |
if (@_) { } |
|
|
205 |
1571 |
elsif (not defined $self->[5]) { } |
|
576
|
16 |
9317 |
if (@_) |
|
585
|
0 |
1925 |
if (@_) |
|
588
|
1925 |
0 |
defined $self->[7] ? : |
|
593
|
1658 |
243 |
if (@_) |
|
595
|
0 |
1658 |
if ($type =~ /:/) { } |
|
606
|
243 |
1658 |
if (defined $self->[7]) |
|
614
|
68 |
51 |
if (@_) |
|
617
|
70 |
49 |
defined $self->[8] ? : |
|
622
|
356 |
64 |
if (@_) |
|
624
|
0 |
356 |
unless ($p =~ /^[012\.]$/) |
|
629
|
386 |
34 |
defined $self->[9] ? : |
|
643
|
0 |
471 |
if defined $self->[8] |
|
644
|
0 |
471 |
if defined $self->[9] |
|
653
|
773 |
0 |
if (ref $s eq ref $self) { } |
|
654
|
0 |
773 |
unless $s->seq_id |
|
655
|
41 |
732 |
unless $s->strand |
|
656
|
0 |
773 |
unless $s->source_tag |
|
669
|
148 |
1067 |
unless $self->[11] |
|
674
|
1067 |
0 |
wantarray ? : |
|
679
|
0 |
0 |
unless $self->[11] |
|
684
|
0 |
0 |
if ($_->[5] eq $id) |
|
690
|
0 |
0 |
if (defined $d) |
|
699
|
68 |
450 |
unless $key and $value |
|
701
|
0 |
450 |
if (exists $self->[10]{$key}) { } |
|
702
|
0 |
0 |
if (ref $self->[10]{$key} eq 'ARRAY') { } |
|
717
|
149 |
366 |
unless $self->[10] |
|
723
|
1 |
423 |
unless $self->[10] |
|
724
|
410 |
13 |
if (exists $self->[10]{$key}) { } |
|
725
|
0 |
410 |
if (ref $self->[10]{$key} eq 'ARRAY') { } |
|
726
|
0 |
0 |
wantarray ? : |
|
739
|
1 |
0 |
unless $self->[10] |
|
740
|
0 |
0 |
wantarray ? : |
|
745
|
34 |
15 |
unless $self->[10] |
|
747
|
15 |
0 |
wantarray ? : |
|
752
|
0 |
0 |
unless $self->[10] |
|
753
|
0 |
0 |
if (exists $self->[10]{$key}) |
|
770
|
0 |
0 |
unless $other and ref $other |
|
771
|
0 |
0 |
unless $self->seq_id eq $other->seq_id |
|
780
|
0 |
0 |
unless $other and ref $other |
|
781
|
0 |
0 |
unless $self->seq_id eq $other->seq_id |
|
790
|
0 |
0 |
unless $other and ref $other |
|
791
|
0 |
0 |
unless $self->seq_id eq $other->seq_id |
|
800
|
0 |
0 |
unless $other and ref $other |
|
801
|
0 |
0 |
unless $self->seq_id eq $other->seq_id |
|
803
|
0 |
0 |
if ($self->start >= $other->start) { } |
|
809
|
0 |
0 |
if ($self->end <= $other->end) { } |
|
815
|
0 |
0 |
if $start > $stop |
|
825
|
0 |
0 |
unless $other and ref $other |
|
826
|
0 |
0 |
unless $self->seq_id eq $other->seq_id |
|
828
|
0 |
0 |
if ($self->start <= $other->start) { } |
|
834
|
0 |
0 |
if ($self->end >= $other->end) { } |
|
840
|
0 |
0 |
if $start > $stop |
|
850
|
0 |
0 |
unless $other and ref $other |
|
851
|
0 |
0 |
unless $self->seq_id eq $other->seq_id |
|
852
|
0 |
0 |
if $self->equals($other) |
|
854
|
0 |
0 |
if ($self->overlaps($other)) { } |
|
856
|
0 |
0 |
if ($self->start < $int->start) |
|
863
|
0 |
0 |
if ($self->end > $int->end) |
|
878
|
0 |
0 |
wantarray ? : |
|
886
|
0 |
2 |
if (@_ and $_[0] ne 3) |
|
900
|
52 |
49 |
if $recurse and $childIDs and not exists $$childIDs{$self->primary_id} |
|
903
|
2 |
47 |
if ($recurse and not defined $childIDs) |
|
912
|
0 |
49 |
defined $self->score ? : |
|
|
0 |
0 |
$self->strand < 0 ? : |
|
|
49 |
0 |
$self->strand > 0 ? : |
|
|
15 |
34 |
defined $self->phase ? : |
|
926
|
49 |
0 |
if ($name) { } |
|
935
|
49 |
0 |
if ($childIDs) |
|
936
|
47 |
2 |
if (exists $$childIDs{$self->primary_id}) |
|
945
|
0 |
41 |
if $tag eq "Name" |
|
946
|
0 |
41 |
if $tag eq "ID" |
|
947
|
14 |
27 |
if $tag eq "Parent" |
|
949
|
0 |
27 |
if (ref $value eq 'ARRAY') { } |
|
960
|
49 |
0 |
if ($recurse) |
|
963
|
47 |
52 |
if $s |
|
985
|
0 |
0 |
defined $self->score ? : |
|
|
0 |
0 |
$self->strand >= 0 ? : |