| line |
true |
false |
branch |
|
22
|
0 |
0 |
if ($rs) { }
|
|
32
|
0 |
0 |
if ($type eq 'raw') { }
|
|
|
0 |
0 |
elsif ($type eq 'vcf') { }
|
|
76
|
0 |
0 |
if /^#/u
|
|
77
|
0 |
0 |
if /^\s*$/u
|
|
82
|
0 |
0 |
unless scalar @fields >= 6
|
|
85
|
0 |
0 |
unless &looks_like_number($fields[1])
|
|
88
|
0 |
0 |
if $fields[1] <= 0
|
|
91
|
0 |
0 |
unless $fields[3] =~ /^(\w+|-)$/u
|
|
94
|
0 |
0 |
unless $fields[4] =~ /^(\w+|-)$/u
|
|
97
|
0 |
0 |
unless $fields[5] =~ /^(HE|HO)$/u
|
|
100
|
0 |
0 |
if ($fields[3] eq $fields[4])
|
|
127
|
0 |
0 |
unless close $fh
|
|
141
|
0 |
0 |
unless ($magic =~ /^##fileformat=VCFv\d+(\.\d+)?$/u)
|
|
154
|
0 |
0 |
if /^##/u
|
|
155
|
0 |
0 |
if /^\s*$/u
|
|
160
|
0 |
0 |
if (/^#/u)
|
|
163
|
0 |
0 |
if ($number_of_fields < 8) { }
|
|
|
0 |
0 |
elsif ($number_of_fields == 8) { }
|
|
|
0 |
0 |
elsif ($number_of_fields == 9) { }
|
|
173
|
0 |
0 |
if (defined $sample_name) { }
|
|
180
|
0 |
0 |
unless (exists $columns{$sample_name})
|
|
193
|
0 |
0 |
unless ($has_header)
|
|
197
|
0 |
0 |
unless scalar @fields > 9
|
|
200
|
0 |
0 |
unless &looks_like_number($fields[1])
|
|
203
|
0 |
0 |
if $fields[1] <= 0
|
|
206
|
0 |
0 |
unless $fields[3] =~ /^(<\w+(:\w+)*>|\w+|-)$/u
|
|
209
|
0 |
0 |
unless $fields[4] =~ /^(\w+|<\w+(:\w+)*>|-|\*)(,(\w+|<\w+(:\w+)*>|-|\*))*$/u
|
|
212
|
0 |
0 |
unless $fields[8] =~ /^GT:?/u
|
|
215
|
0 |
0 |
unless $fields[$sample_i] =~ m[^[0-9.]+([/\|][0-9.])?:*]u
|
|
218
|
0 |
0 |
if ($fields[3] eq $fields[4])
|
|
225
|
0 |
0 |
if ($fields[3] =~ /<\w+>/u or $fields[4] =~ /<\w+>/u)
|
|
230
|
0 |
0 |
if ($fields[4] =~ /\*/u)
|
|
241
|
0 |
0 |
if ($g1 eq "." or defined $g2 and $g2 eq ".")
|
|
246
|
0 |
0 |
if (not defined $g2 or $g1 == $g2) { }
|
|
248
|
0 |
0 |
if $g1 == 0
|
|
254
|
0 |
0 |
$g1 > $g2 ? :
|
|
283
|
0 |
0 |
unless close $fh
|
|
304
|
0 |
0 |
if ($next_snv->{'low'} > $high)
|
|
337
|
0 |
0 |
if ($blacklist{&refaddr($prev_snv)})
|
|
344
|
0 |
0 |
if ($i == $j or $blacklist{&refaddr($next_snv)})
|
|
349
|
0 |
0 |
if ($next_snv->{'ref'} eq '-' and $prev_snv->{'ref'} eq '-' and $next_snv->{'pos'} != $prev_snv->{'pos'}) { }
|
|
|
0 |
0 |
elsif ($next_snv->{'ref'} eq '-' and $prev_snv->{'ref'} ne '-' and $next_snv->{'pos'} < $prev_snv->{'pos'}) { }
|
|
363
|
0 |
0 |
length $_ > 25 ? :
|
|
368
|
0 |
0 |
if ($prev_size >= $next_size) { }
|
|
369
|
0 |
0 |
if ($variation_file) { }
|
|
383
|
0 |
0 |
if ($variation_file) { }
|
|
414
|
0 |
0 |
unless defined $rs
|
|
417
|
0 |
0 |
unless defined $compressed
|
|
428
|
0 |
0 |
if (scalar @$structural_variation > 1)
|
|
443
|
0 |
0 |
unless defined $rs
|
|
446
|
0 |
0 |
unless $rs->is_user_provided
|
|
470
|
0 |
0 |
if ($entry) { }
|
|
498
|
0 |
0 |
$structural_variation->is_user_provided ? :
|