| line |
!l |
l&&!r |
l&&r |
condition |
|
224
|
290 |
0 |
1 |
$feats and ref $feats eq 'ARRAY' |
|
232
|
282 |
0 |
9 |
$seqs and ref $seqs eq 'ARRAY' |
|
279
|
0 |
2420 |
0 |
ref $seq and $seq->isa('Bio::LocatableSeq') |
|
352
|
0 |
0 |
13 |
ref $seq and $seq->isa('Bio::LocatableSeq') |
|
437
|
0 |
147 |
6387 |
$one[$k] ne '.' and $one[$k] ne '-' |
|
|
147 |
0 |
6387 |
$one[$k] ne '.' and $one[$k] ne '-' and defined $two[$k] |
|
|
147 |
2058 |
4329 |
$one[$k] ne '.' and $one[$k] ne '-' and defined $two[$k] and $one[$k] eq $two[$k] |
|
441
|
0 |
147 |
6387 |
$one[$k] ne '.' and $one[$k] ne '-' |
|
|
147 |
0 |
6387 |
$one[$k] ne '.' and $one[$k] ne '-' and defined $two[$k] |
|
|
147 |
0 |
6387 |
$one[$k] ne '.' and $one[$k] ne '-' and defined $two[$k] and $two[$k] ne '.' |
|
|
0 |
67 |
6320 |
$one[$k] ne '.' and $one[$k] ne '-' and defined $two[$k] and $two[$k] ne '.' and $two[$k] ne '-' |
|
566
|
6 |
5 |
1 |
$is_num and $pos == $seqid |
|
834
|
0 |
0 |
258 |
$pos =~ /^\d+$/ and $pos > 0 |
|
972
|
0 |
0 |
1 |
$start =~ /^\d+$/ and $start > 0 |
|
974
|
0 |
0 |
1 |
$end =~ /^\d+$/ and $end > 0 |
|
1026
|
0 |
0 |
32 |
/^\d+$/ and $_ > 0 |
|
|
0 |
0 |
32 |
/^\d+$/ and $_ > 0 and $_ <= $end |
|
1086
|
0 |
0 |
31 |
$start =~ /^\d+$/ and $start > 0 |
|
1088
|
0 |
0 |
31 |
$end =~ /^\d+$/ and $end > 0 |
|
1136
|
38 |
15 |
2 |
defined $seq->strand and $seq->strand < 0 |
|
1149
|
0 |
1 |
106 |
$new_seq->start and $new_seq->end >= $new_seq->start |
|
1454
|
0 |
0 |
4 |
defined $from and defined $to |
|
1535
|
20 |
4 |
4 |
${$cigars{$name};}[$x - 1] + 1 < do {
$cigars{$name}
}->[$x] and ${$cigars{$name};}[$x + 1] > do {
$cigars{$name}
}->[$x] + 1 |
|
1545
|
24 |
4 |
8 |
do {
$cigars{$name}
}->[$x] == ${$cigars{$name};}[$x - 1] + 1 and do {
$cigars{$name}
}->[$x] == ${$cigars{$name};}[$x + 1] - 1 |
|
1706
|
18 |
3 |
1 |
exists $gap_hsh{$pos} and $gap_hsh{$pos} == scalar @seqs |
|
1782
|
0 |
720 |
0 |
defined $refseq[$i] and $refseq[$i] =~ /[A-Za-z\*]/ || $refseq[$i] =~ /$gapchar/ |
|
|
0 |
196 |
524 |
defined $refseq[$i] and $refseq[$i] =~ /[A-Za-z\*]/ || $refseq[$i] =~ /$gapchar/ and $refseq[$i] eq $varseq[$i] |
|
1822
|
0 |
19782 |
0 |
defined $refseq[$i] and $refseq[$i] =~ /[A-Za-z\*]/ || $refseq[$i] =~ /$gapchar/ |
|
|
528 |
5474 |
13780 |
defined $refseq[$i] and $refseq[$i] =~ /[A-Za-z\*]/ || $refseq[$i] =~ /$gapchar/ and $varseq[$i] eq $match |
|
2087
|
1357 |
1069 |
2472 |
$hash{$key} > $count and $hash{$key} >= $threshold |
|
2232
|
7 |
0 |
0 |
$rna and $char eq 'T' |
|
2253
|
0 |
0 |
17 |
ref $meta && $meta->isa('Bio::Seq::MetaI') |
|
|
39 |
17 |
0 |
$meta and not ref $meta && $meta->isa('Bio::Seq::MetaI') |
|
2558
|
15 |
3 |
0 |
$length_measure and not exists $enum{$length_measure} |
|
2707
|
438 |
0 |
112 |
$disname and $name |
|
2753
|
1 |
15 |
0 |
defined $name and $name eq $seq->id |
|
2986
|
0 |
14 |
0 |
$a1 and $a2 |
|
|
0 |
14 |
0 |
$a1 and $a2 and $ref |
|
2994
|
0 |
14 |
0 |
$refseq and $allele1 |
|
|
0 |
14 |
0 |
$refseq and $allele1 and $allele2 |
|
3005
|
14 |
14 |
182 |
$compres eq $res1 && $compres eq $res2 |
|
3242
|
0 |
0 |
6 |
$start =~ /^\d+$/ and $start > 0 |
|
|
0 |
0 |
6 |
$start =~ /^\d+$/ and $start > 0 and $start <= $self->length |
|
3245
|
0 |
0 |
6 |
$end =~ /^\d+$/ and $end > 0 |
|
|
0 |
0 |
6 |
$end =~ /^\d+$/ and $end > 0 and $end <= $self->length |
|
3250
|
0 |
0 |
6 |
CORE::length $mask_char == 1 and not $mask_char =~ /$nonres/ |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
289
|
2414 |
5 |
0 |
$seq->id || $seq->display_id || $seq->primary_id |
|
559
|
0 |
0 |
1 |
$seqid <= 1 or $seqid > $self->num_sequences |
|
566
|
1 |
1 |
10 |
$is_num and $pos == $seqid or $seqid eq $seq[$i]->display_id |
|
1233
|
1 |
5 |
0 |
$gapchar || $self->gap_char |
|
1608
|
12 |
0 |
3120 |
$refchar eq '-' || $refchar eq '.' || $refchar eq ' ' |
|
1611
|
2295 |
99 |
24512 |
$seq->[$pos] eq '-' or $seq->[$pos] eq '.' |
|
|
2394 |
0 |
24512 |
$seq->[$pos] eq '-' or $seq->[$pos] eq '.' or $seq->[$pos] eq ' ' |
|
1669
|
0 |
14 |
0 |
$gapchar || $self->gap_char |
|
1696
|
1 |
1 |
0 |
$gapchar || $self->gap_char |
|
1730
|
0 |
0 |
0 |
$gapchar || $self->gap_char |
|
1782
|
705 |
15 |
0 |
$refseq[$i] =~ /[A-Za-z\*]/ || $refseq[$i] =~ /$gapchar/ |
|
1822
|
19011 |
243 |
528 |
$refseq[$i] =~ /[A-Za-z\*]/ || $refseq[$i] =~ /$gapchar/ |
|
1963
|
25 |
26 |
11191 |
defined $char or not defined $self->{'_gap_char'} |
|
2104
|
4435 |
309 |
17334 |
$letter eq $gapchar or $letter =~ /\./ |
|
2596
|
16 |
16 |
60 |
$length_measure eq 'short' or $length_measure eq 'long' |
|
2599
|
1 |
4 |
11 |
not defined $len or $seq_len < $len |
|
2603
|
1 |
1 |
14 |
not defined $len or $seq_len > $len |
|
3033
|
4 |
0 |
0 |
not defined $filter_cb or ref $filter_cb eq 'CODE' |