| line |
true |
false |
branch |
|
124
|
4 |
42 |
defined $coord_style ? : |
|
126
|
4 |
42 |
defined $track ? : |
|
128
|
14 |
32 |
defined $qual_levels ? : |
|
129
|
46 |
0 |
if defined $qual_levels |
|
130
|
43 |
3 |
if defined $reference |
|
131
|
5 |
41 |
if defined $mid |
|
133
|
24 |
22 |
if defined $errors |
|
159
|
48 |
105 |
if (defined $qual_levels) |
|
160
|
0 |
48 |
if (scalar @$qual_levels != 0 and scalar @$qual_levels != 2) |
|
185
|
45 |
308 |
if (defined $reference) |
|
187
|
0 |
3 |
unless ($reference->isa('Bio::SeqI') or $reference->isa('Bio::PrimarySeqI')) |
|
191
|
0 |
45 |
if ($self->{'mid'} or $self->{'errors'}) |
|
196
|
40 |
5 |
unless (defined $self->start) |
|
200
|
40 |
5 |
unless (defined $self->end) |
|
204
|
39 |
6 |
unless (defined $self->strand) |
|
211
|
13 |
32 |
if scalar @{$self->qual_levels;} |
|
212
|
44 |
1 |
if $self->track |
|
224
|
4 |
41 |
if ($self->strand == -1) |
|
245
|
43 |
2 |
if (defined $ref_id) |
|
250
|
41 |
4 |
if ($self->coord_style eq 'bioperl') { } |
|
252
|
41 |
0 |
if (defined $strand) |
|
254
|
38 |
3 |
if $strand == 1 |
|
258
|
1 |
3 |
if (defined $strand and $strand == -1) { } |
|
268
|
42 |
3 |
if (defined $self->reference->desc and not $self->reference->desc =~ /^\s*$/) |
|
293
|
8 |
3 |
if (defined $mid) |
|
295
|
0 |
8 |
unless (defined $self->reference) |
|
300
|
0 |
8 |
if ($self->{'errors'}) |
|
305
|
0 |
8 |
unless ($self->validate_seq($mid)) |
|
310
|
4 |
4 |
if scalar @{$self->qual_levels;} |
|
311
|
8 |
0 |
if $self->track |
|
325
|
2 |
6 |
if (defined $old_mid) |
|
341
|
1 |
3 |
if (defined $old_mid) |
|
353
|
7 |
2 |
if ($mid) |
|
391
|
28 |
65 |
if (defined $errors) |
|
393
|
0 |
28 |
unless (defined ref $errors and ref $errors eq 'HASH') |
|
397
|
0 |
28 |
unless (defined $self->reference) |
|
407
|
0 |
28 |
if ($self->{'_mutated'}) |
|
409
|
0 |
0 |
if scalar @{$self->qual_levels;} |
|
410
|
0 |
0 |
if $self->track |
|
414
|
6 |
22 |
if scalar @{$self->qual_levels;} |
|
415
|
28 |
0 |
if $self->track |
|
427
|
36 |
4 |
if (ref $res eq '') |
|
429
|
11 |
25 |
if scalar @$arr == 0 |
|
448
|
3 |
35 |
if (defined $read_length and $pos > $read_length) |
|
455
|
2 |
1 |
if ($pos < 1 and exists $ops->{'%'} || exists $ops->{'-'}) |
|
462
|
0 |
0 |
if ($pos < 0 and exists $ops->{'+'}) |
|
470
|
0 |
38 |
if (not exists $valid_ops{$op}) { } |
|
476
|
0 |
38 |
if ($op eq '%' and scalar @$res < 1) |
|
481
|
0 |
38 |
if ($op eq '+' and scalar @$res < 1) |
|
486
|
0 |
38 |
if ($op eq '-' and scalar @$res < 1) |
|
493
|
2 |
36 |
unless scalar keys %$ops |
|
504
|
22 |
6 |
if (scalar keys %$errors > 0) { } |
|
509
|
64 |
35 |
unless exists $errors->{$pos}{$type} |
|
511
|
9 |
26 |
if ($type eq '%') { } |
|
|
10 |
16 |
elsif ($type eq '-') { } |
|
|
16 |
0 |
elsif ($type eq '+') { } |
|
540
|
6 |
0 |
if (scalar keys %$errors > 0) |
|
545
|
20 |
10 |
unless exists $errors->{$pos}{$type} |
|
547
|
3 |
7 |
if ($type eq '%') { } |
|
|
2 |
5 |
elsif ($type eq '-') { } |
|
|
5 |
0 |
elsif ($type eq '+') { } |
|
571
|
23 |
6 |
if (defined $errors and scalar keys %$errors > 0) |
|
577
|
66 |
36 |
unless exists $errors->{$pos}{$type} |
|
579
|
11 |
39 |
unless defined $val |
|
606
|
48 |
86 |
if (defined $track) |
|
607
|
2 |
46 |
if (defined $self->reference) |
|
608
|
1 |
1 |
if ($track == 1) { } |
|
643
|
46 |
45 |
if (defined $coord_style) |
|
644
|
0 |
46 |
unless (exists $styles{$coord_style}) |