| line |
true |
false |
branch |
|
174
|
0 |
2 |
unless defined $line and defined $event_type |
|
202
|
1 |
14 |
defined $extended_fields{$key} ? : |
|
256
|
0 |
0 |
if ($self->isFlagged($flags{'REVERSE_COMPLEMENTED'})) { } |
|
272
|
0 |
0 |
if ($self->isFlagged($flags{'REVERSE_COMPLEMENTED'})) { } |
|
306
|
0 |
0 |
unless defined $line_number |
|
307
|
0 |
0 |
if ($self->updatedLine ne $self->line) { } |
|
347
|
1 |
2 |
if (defined $updated_line) { } |
|
|
1 |
1 |
elsif (not defined $$self{'updated_line'}) { } |
|
368
|
1 |
2 |
if (defined $new_qname) |
|
385
|
1 |
5 |
if (defined $new_flag) |
|
402
|
3 |
3 |
if (defined $new_rname) |
|
432
|
1 |
2 |
if (defined $new_pos) |
|
449
|
1 |
2 |
if (defined $new_mapq) |
|
466
|
1 |
3 |
if (defined $new_cigar) |
|
483
|
1 |
2 |
if (defined $new_rnext) |
|
500
|
1 |
2 |
if (defined $new_pnext) |
|
517
|
1 |
2 |
if (defined $new_tlen) |
|
536
|
1 |
3 |
if (defined $new_seq) |
|
553
|
1 |
2 |
if (defined $new_qual) |
|
570
|
0 |
0 |
unless defined $field |
|
592
|
1 |
0 |
if (defined $$self{'extended_fields'}{'SA'}) |
|
598
|
1 |
1 |
if ($strand eq '+') { } |
|
636
|
2 |
1 |
unless defined $ops_occ{$op} |
|
681
|
1 |
0 |
if (defined $$self{'extended_fields'}{'XP'}{'chimera'}) { } |
|
707
|
1 |
2 |
if (defined $$self{'extended_fields'}{'XP'}{'loc'} and ref $$self{'extended_fields'}{'XP'}{'loc'} ne 'HASH') |
|
735
|
0 |
2 |
if (not defined $key) { } |
|
|
1 |
1 |
elsif (defined $value) { } |
|
766
|
0 |
2 |
unless defined $class |
|
768
|
1 |
1 |
if ($class eq 'unique') { } |
|
|
0 |
1 |
elsif ($class eq 'duplicated') { } |
|
|
1 |
0 |
elsif ($class eq 'multiple') { } |
|
|
0 |
0 |
elsif ($class eq 'normal') { } |
|
|
0 |
0 |
elsif ($class eq 'almostNormal') { } |
|
809
|
3 |
0 |
if (defined $$self{'events'}{$event_type}) { } |
|
831
|
2 |
1 |
if (defined $event_type_to_load and defined $$self{$event_type_to_load}{'loaded'}) |
|
834
|
1 |
0 |
if (not defined $$self{'events'} and defined $$self{'extended_fields'}{'XE'}) |
|
839
|
0 |
1 |
if defined $event_type_to_load and $event_type ne $event_type_to_load |
|
840
|
1 |
0 |
if (defined $event_id) |
|
842
|
1 |
0 |
if ($event_type eq 'Junction') { } |
|
|
0 |
0 |
elsif ($event_type eq 'Ins' or $event_type eq 'Del') { } |
|
|
0 |
0 |
elsif ($event_type eq 'SNP') { } |
|
|
0 |
0 |
elsif ($event_type eq 'Error') { } |
|
|
0 |
0 |
elsif ($event_type eq 'chimera') { } |
|
|
0 |
0 |
elsif ($event_type eq 'Undetermined') { } |
|
|
0 |
0 |
elsif ($event_type eq 'BioUndetermined') { } |
|
892
|
1 |
0 |
if (keys %event_hash > 1) |
|
901
|
1 |
0 |
if (defined $event_type_to_load) { } |
|
925
|
1 |
1 |
if (defined $$self{'events'}{$event_type}) { } |
|
944
|
2 |
0 |
if (defined $type and defined $$self{'events'}{$type}) |
|
947
|
2 |
0 |
if ($event eq $delete_event) |
|
973
|
1 |
0 |
if ($self->removeEvent($event)) { } |
|
979
|
1 |
0 |
if ($new_event_type eq 'Junction') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'Ins' or $new_event_type eq 'Del') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'SNP') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'Error') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'chimera') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'Undetermined') { } |
|
|
0 |
0 |
elsif ($new_event_type eq 'BioUndetermined') { } |
|
1046
|
1 |
1 |
if (not defined $$self{'sam_detailed'}) |
|
1052
|
1 |
1 |
if ($k eq 'p_loc') { } |
|
|
1 |
0 |
elsif ($k eq 'p_support') { } |
|
1076
|
1 |
3 |
if (defined $$self{'extended_fields'}{'XP'} and ref $$self{'extended_fields'}{'XP'} ne 'HASH') |
|
1116
|
0 |
1 |
unless defined $chr and defined $pos and defined $strand |