| line |
true |
false |
branch |
|
82
|
1 |
66 |
unless (grep /^$input$/u, @valid_new_attributes) |
|
89
|
0 |
44 |
unless (defined $self->{'filename'}) |
|
93
|
1 |
43 |
unless (-e $self->{'filename'}) |
|
100
|
0 |
43 |
unless $abif->open_abif($self->{'filename'}) |
|
104
|
0 |
43 |
unless ($try) |
|
116
|
33 |
10 |
unless defined $object->{'trim_ends'} |
|
117
|
41 |
2 |
unless defined $object->{'wnd'} |
|
118
|
37 |
6 |
unless defined $object->{'min_qual'} |
|
119
|
41 |
2 |
unless defined $object->{'bad_bases'} |
|
120
|
41 |
2 |
unless defined $object->{'keep_abi'} |
|
126
|
42 |
1 |
if ($self->{'keep_abi'} == 0) |
|
134
|
0 |
946 |
unless (grep /^$input$/u, @valid_new_attributes, @valid_obj_attributes) |
|
147
|
0 |
16 |
if (not defined $name) { } |
|
|
0 |
16 |
elsif ($name =~ /\s+/u) { } |
|
154
|
12 |
4 |
if (defined $quality_value) |
|
155
|
4 |
8 |
if ($quality_value =~ /^\d+$/u and $quality_value >= 10) { } |
|
|
4 |
4 |
elsif (length $quality_value == 1) { } |
|
156
|
4 |
0 |
$quality_value <= 93 ? : |
|
166
|
3 |
9 |
if ($self->{'iso_seq'}) { } |
|
216
|
612 |
195 |
if $base1 ne "-" |
|
217
|
677 |
130 |
if $base2 ne "-" |
|
219
|
481 |
326 |
if ($base1 eq $base2) { } |
|
|
195 |
131 |
elsif ($base1 eq '-' and $base2 ne '-') { } |
|
|
130 |
1 |
elsif ($base1 ne '-' and $base2 eq '-') { } |
|
|
1 |
0 |
elsif ($base1 ne '-' and $base2 ne '-') { } |
|
228
|
0 |
1 |
_ascii_qual($qual1) > _ascii_qual($qual2) ? : |
|
275
|
32692 |
0 |
$_ <= 93 ? : |
|
287
|
39 |
4 |
if ($self->{'trim_ends'}) |
|
308
|
39 |
0 |
if ($begin_pos > 0 and $end_pos > 0) { } |
|
318
|
14 |
29 |
if (not $self->{'sequence'} =~ /[ACGT][RYMKWS]+[ACGT]/iu) { } |
|
334
|
74 |
27206 |
if ($iupac{$s0}) { } |
|
349
|
14 |
29 |
if ($seq1 eq $seq2) { } |
|
364
|
2 |
0 |
unless defined $offset |