| line |
true |
false |
branch |
|
25
|
14 |
62 |
if (substr($_[0], 0, 1) eq '-') { } |
|
|
62 |
0 |
elsif (not defined $seq) { } |
|
29
|
13 |
38 |
if ($i =~ /^-(seq|sequence)/u) { } |
|
|
11 |
27 |
elsif ($i =~ /^-(name|id)/u) { } |
|
|
7 |
20 |
elsif ($i =~ /^-(comment|desc|description)/u) { } |
|
|
13 |
7 |
elsif ($i =~ /^-qual(ity)?/u) { } |
|
|
4 |
3 |
elsif ($i =~ /^-offset/u) { } |
|
|
2 |
1 |
elsif ($i =~ /^-line_len/u) { } |
|
|
0 |
1 |
elsif ($i =~ /^-default_quality/u) { } |
|
50
|
1 |
61 |
if scalar @_ < 1 or scalar @_ > 4 |
|
55
|
0 |
74 |
unless (defined $seq) |
|
60
|
2 |
72 |
if (defined $seq and defined $qual and length $seq != length $qual) |
|
96
|
1 |
76 |
if defined $new_val |
|
105
|
0 |
10 |
if defined $new_val |
|
114
|
0 |
48 |
if defined $new_val |
|
122
|
0 |
7 |
if defined $new_val |
|
130
|
0 |
21 |
if defined $new_val and not $new_val =~ /^\d+$/u |
|
131
|
1 |
20 |
if defined $new_val |
|
139
|
0 |
12 |
if defined $new_val and not $new_val =~ /^\d+$/u |
|
140
|
0 |
12 |
if defined $new_val |
|
148
|
0 |
6 |
if defined $new_val and length $new_val != 1 |
|
149
|
0 |
6 |
if defined $new_val |
|
168
|
2 |
0 |
if defined reverse($self->{'qual'}) |
|
178
|
0 |
1 |
if ($self->{'seq'} =~ /U/iu) { } |
|
193
|
4 |
3 |
if (defined $len) { } |
|
195
|
1 |
3 |
defined $self->{'qual'} ? : |
|
198
|
1 |
2 |
defined $self->{'qual'} ? : |
|
207
|
0 |
42 |
if length $quality_encoded != 1 |
|
208
|
42 |
0 |
defined $offset ? : |
|
215
|
0 |
2 |
unless $quality_integer =~ /^\d+$/u |
|
216
|
2 |
0 |
defined $offset ? : |
|
225
|
5 |
0 |
if (defined $self->{'qual'}) |
|
255
|
0 |
1 |
unless $qual_value =~ /^\d+$/u |
|
260
|
1 |
6 |
if ($qualities[$i] <= $qual_value) |
|
275
|
0 |
1 |
unless $qual_value =~ /^\d+$/u |
|
280
|
1 |
2 |
if ($qualities[$i] >= $qual_value) |
|
300
|
6 |
0 |
if (exists $baseVal{substr $kmer, $i, 1}) { } |
|
353
|
0 |
1 |
unless $self->{'seq'} =~ /^[ACGTU]+$/iu |
|
360
|
2 |
0 |
if ($num != -1) { } |
|
381
|
0 |
0 |
if (defined $self->{'qual'}) { } |
|
403
|
6 |
9 |
defined $self->{'comment'} && length $self->{'comment'} > 0 ? : |
|
413
|
15 |
10 |
if (defined $user_quality) { } |
|
|
6 |
4 |
elsif (not defined $quality) { } |
|
415
|
10 |
5 |
if (length $user_quality == 1) { } |
|
428
|
10 |
15 |
defined $self->{'comment'} && length $self->{'comment'} > 0 ? : |
|
453
|
6 |
7 |
defined $self->{'qual'} > 0 && length $self->{'qual'} == length $self->{'seq'} ? : |
|
460
|
4 |
3 |
defined $self->{'qual'} > 0 && length $self->{'qual'} == length $self->{'seq'} ? : |
|
466
|
10 |
5 |
if (not defined $width or $width == 0) |