| line |
true |
false |
branch |
|
37
|
0 |
59 |
defined $validate ? : |
|
39
|
0 |
59 |
if $header |
|
41
|
59 |
0 |
if (not defined $self->sequence_factory) |
|
80
|
388 |
1520 |
if ($mode eq '-seq' and $line =~ /^@([^\n]+)$/mosx) { } |
|
|
384 |
1136 |
elsif ($mode eq '-seq' and $line =~ /^\+([^\n]*)/mosx) { } |
|
83
|
388 |
0 |
if ($$data{-'descriptor'} =~ /^\s*(\S+)\s*(.*)/) { } |
|
93
|
0 |
384 |
unless $$data{-'descriptor'} |
|
94
|
2 |
382 |
if ($desc and $$data{-'descriptor'} ne $desc) |
|
100
|
352 |
395 |
if ($mode eq '-raw_quality' and defined $$data{-'raw_quality'} and length $$data{-'raw_quality'} >= length $$data{-'seq'}) |
|
106
|
3 |
781 |
if ($line =~ /^$/) |
|
113
|
31 |
1520 |
unless (defined $line) |
|
119
|
14 |
386 |
unless $data |
|
120
|
6 |
380 |
unless ($$data{-'seq'} and defined $$data{-'raw_quality'}) |
|
125
|
3 |
377 |
if (length $$data{-'seq'} != length $$data{-'raw_quality'}) |
|
132
|
9 |
69667 |
if ($self->{'_validate_qual'} and not exists $self->{'chr2qual'}{$_}) |
|
139
|
523 |
69144 |
$self->variant eq 'solexa' ? : |
|
151
|
0 |
9 |
unless ($seq->isa('Bio::Seq::Quality')) |
|
163
|
6 |
3 |
if (my $desc = $seq->desc) |
|
171
|
2 |
6 |
$var eq 'solexa' ? : |
|
|
1 |
8 |
$ns eq 'solexa' && $var eq 'solexa' ? : |
|
175
|
92 |
451 |
if $var ne 'solexa' and $ns eq 'solexa' |
|
176
|
481 |
62 |
if (exists $qual_map->{$q}) { } |
|
183
|
0 |
62 |
if (exists $self->{'fuzzy_qual2chr'}{$bounds}) { } |
|
188
|
0 |
62 |
$q <= $self->{'qual_start'} ? : |
|
194
|
2 |
7 |
if ($self->{'_validate_qual'} and %bad_qual) |
|
198
|
0 |
9 |
unless $self->_print('@', $top, "\n", $str, "\n") |
|
199
|
0 |
9 |
$self->{'_quality_header'} ? : |
|
|
0 |
9 |
unless $self->_print('+', $self->{'_quality_header'} ? $top : '', "\n", $qual, "\n") |
|
211
|
0 |
0 |
unless (exists $self->{'fasta_proxy'}) |
|
219
|
0 |
0 |
unless (exists $self->{'qual_proxy'}) |
|
232
|
10 |
49 |
if ($var eq 'solexa') { } |
|
246
|
50 |
630 |
if $q < 0 |
|
247
|
20 |
610 |
$q <= 1 ? : |
|
265
|
59 |
0 |
if (defined $val) |
|
273
|
0 |
0 |
if (defined $val) |