| line |
true |
false |
branch |
|
34
|
0 |
2 |
unless defined $line and defined $event_type |
|
50
|
1 |
15 |
defined $extended_fields{$key} ? : |
|
85
|
0 |
0 |
if ($self->isFlagged($flags{'REVERSE_COMPLEMENTED'})) { } |
|
95
|
0 |
0 |
if ($self->isFlagged($flags{'REVERSE_COMPLEMENTED'})) { } |
|
112
|
0 |
0 |
unless defined $line_number |
|
113
|
0 |
0 |
if ($self->updatedLine ne $self->line) { } |
|
135
|
1 |
2 |
if (defined $updated_line) { } |
|
|
1 |
1 |
elsif (not defined $self->{'updated_line'}) { } |
|
149
|
1 |
2 |
if (defined $new_qname) |
|
159
|
1 |
5 |
if (defined $new_flag) |
|
169
|
3 |
4 |
if (defined $new_rname) |
|
185
|
1 |
2 |
if (defined $new_pos) |
|
195
|
1 |
2 |
if (defined $new_mapq) |
|
205
|
1 |
3 |
if (defined $new_cigar) |
|
215
|
1 |
2 |
if (defined $new_rnext) |
|
225
|
1 |
2 |
if (defined $new_pnext) |
|
235
|
1 |
2 |
if (defined $new_tlen) |
|
245
|
1 |
3 |
if (defined $new_seq) |
|
255
|
1 |
2 |
if (defined $new_qual) |
|
265
|
0 |
1 |
unless defined $field |
|
274
|
1 |
0 |
if (defined $self->{'extended_fields'}{'SA'}) |
|
280
|
1 |
1 |
if ($strand eq '+') { } |
|
305
|
2 |
1 |
unless defined $ops_occ{$op} |
|
329
|
1 |
0 |
if (defined $self->{'extended_fields'}{'XP'}{'chimera'}) { } |
|
343
|
1 |
2 |
if (defined $self->{'extended_fields'}{'XP'}{'loc'} and ref $self->{'extended_fields'}{'XP'}{'loc'} ne 'HASH') |
|
355
|
0 |
2 |
if (not defined $key) { } |
|
|
1 |
1 |
elsif (defined $value) { } |
|
369
|
0 |
2 |
unless defined $class |
|
371
|
1 |
1 |
if ($class eq 'unique') { } |
|
|
0 |
1 |
elsif ($class eq 'duplicated') { } |
|
|
1 |
0 |
elsif ($class eq 'multiple') { } |
|
|
0 |
0 |
elsif ($class eq 'normal') { } |
|
|
0 |
0 |
elsif ($class eq 'almostNormal') { } |
|
378
|
0 |
0 |
defined $self->{'extended_fields'}{'XN'} ? : |
|
380
|
0 |
0 |
defined $self->{'extended_fields'}{'XN'} ? : |
|
391
|
3 |
0 |
if (defined $self->{'events'}{$event_type}) { } |
|
406
|
1 |
2 |
if (not defined $self->{'events'} and defined $self->{'extended_fields'}{'XE'}) |
|
412
|
0 |
1 |
if defined $event_type_to_load and $event_type ne $event_type_to_load |
|
413
|
1 |
0 |
if (defined $event_id) |
|
415
|
1 |
0 |
if ($event_type eq 'junction') { } |
|
|
0 |
0 |
elsif ($event_type eq 'ins' or $event_type eq 'del') { } |
|
|
0 |
0 |
elsif ($event_type eq 'snp') { } |
|
|
0 |
0 |
elsif ($event_type eq 'error') { } |
|
|
0 |
0 |
elsif ($event_type eq 'chimera') { } |
|
|
0 |
0 |
elsif ($event_type eq 'undetermined') { } |
|
|
0 |
0 |
elsif ($event_type eq 'bioundetermined') { } |
|
467
|
1 |
0 |
if (keys %event_hash > 1) |
|
490
|
0 |
2 |
if (defined $self->{'events'}{$event_type}) { } |
|
502
|
1 |
1 |
if (defined $type and defined $self->{'events'}{$type}) |
|
505
|
1 |
0 |
if ($event eq $delete_event) |
|
527
|
1 |
0 |
if ($self->removeEvent($event)) { } |
|
533
|
1 |
0 |
if ($new_event_type eq 'Junction') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'Ins' or $new_event_type eq 'Del') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'SNP') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'Error') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'chimera') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'Undetermined') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'BioUndetermined') { } |
|
592
|
1 |
1 |
if (not defined $self->{'sam_detailed'}) |
|
598
|
1 |
1 |
if ($k eq 'p_loc') { } |
|
|
1 |
0 |
elsif ($k eq 'p_support') { } |
|
614
|
1 |
3 |
if (defined $self->{'extended_fields'}{'XP'} and ref $self->{'extended_fields'}{'XP'} ne 'HASH') |
|
634
|
0 |
1 |
unless defined $chr and defined $pos and defined $strand |