| line |
true |
false |
branch |
|
24
|
1 |
80 |
unless (defined $_[0]) |
|
28
|
15 |
65 |
if (substr($_[0], 0, 1) eq '-') { } |
|
|
65 |
0 |
elsif (not defined $seq) { } |
|
32
|
15 |
38 |
if ($i =~ /^-(seq|sequence)/u) { } |
|
|
12 |
26 |
elsif ($i =~ /^-(name|id)/u) { } |
|
|
7 |
19 |
elsif ($i =~ /^-(comment|desc|description)/u) { } |
|
|
13 |
6 |
elsif ($i =~ /^-qual(ity)?/u) { } |
|
|
3 |
3 |
elsif ($i =~ /^-offset/u) { } |
|
|
2 |
1 |
elsif ($i =~ /^-line_len/u) { } |
|
|
0 |
1 |
elsif ($i =~ /^-default_quality/u) { } |
|
53
|
0 |
65 |
if scalar @_ < 1 or scalar @_ > 4 |
|
58
|
0 |
79 |
unless (defined $seq) |
|
63
|
2 |
77 |
if (defined $seq and defined $qual and length $seq != length $qual) |
|
99
|
5 |
88 |
if defined $new_val |
|
108
|
0 |
14 |
if defined $new_val |
|
117
|
0 |
56 |
if defined $new_val |
|
125
|
0 |
11 |
if defined $new_val |
|
133
|
0 |
29 |
if defined $new_val and not $new_val =~ /^\d+$/u |
|
134
|
1 |
28 |
if defined $new_val |
|
142
|
0 |
20 |
if defined $new_val and not $new_val =~ /^\d+$/u |
|
143
|
0 |
20 |
if defined $new_val |
|
151
|
0 |
10 |
if defined $new_val and length $new_val != 1 |
|
152
|
0 |
10 |
if defined $new_val |
|
171
|
2 |
0 |
if defined reverse($self->{'qual'}) |
|
181
|
0 |
1 |
if ($self->{'seq'} =~ /U/iu) { } |
|
196
|
4 |
3 |
if (defined $len) { } |
|
198
|
1 |
3 |
defined $self->{'qual'} ? : |
|
201
|
1 |
2 |
defined $self->{'qual'} ? : |
|
210
|
0 |
42 |
if length $quality_encoded != 1 |
|
211
|
42 |
0 |
defined $offset ? : |
|
218
|
0 |
2 |
unless $quality_integer =~ /^\d+$/u |
|
219
|
2 |
0 |
defined $offset ? : |
|
228
|
5 |
0 |
if (defined $self->{'qual'}) |
|
258
|
0 |
1 |
unless $qual_value =~ /^\d+$/u |
|
263
|
1 |
6 |
if ($qualities[$i] <= $qual_value) |
|
278
|
0 |
1 |
unless $qual_value =~ /^\d+$/u |
|
283
|
1 |
2 |
if ($qualities[$i] >= $qual_value) |
|
303
|
66 |
0 |
if (exists $baseVal{substr $kmer, $i, 1}) { } |
|
356
|
0 |
5 |
unless $self->{'seq'} =~ /^[ACGTU]+$/iu |
|
363
|
22 |
0 |
if ($num != -1) { } |
|
384
|
0 |
0 |
if (defined $self->{'qual'}) { } |
|
406
|
6 |
9 |
defined $self->{'comment'} && length $self->{'comment'} > 0 ? : |
|
416
|
15 |
10 |
if (defined $user_quality) { } |
|
|
6 |
4 |
elsif (not defined $quality) { } |
|
418
|
10 |
5 |
if (length $user_quality == 1) { } |
|
422
|
5 |
0 |
unless ($FASTX::Seq::QUIET) |
|
433
|
10 |
15 |
defined $self->{'comment'} && length $self->{'comment'} > 0 ? : |
|
458
|
6 |
7 |
defined $self->{'qual'} > 0 && length $self->{'qual'} == length $self->{'seq'} ? : |
|
465
|
4 |
3 |
defined $self->{'qual'} > 0 && length $self->{'qual'} == length $self->{'seq'} ? : |
|
471
|
10 |
5 |
if (not defined $width or $width == 0) |