| line |
true |
false |
branch |
|
229
|
0 |
12 |
unless defined $input{'pA'} and defined $input{'pC'} and defined $input{'pG'} and defined $input{'pT'} |
|
233
|
11 |
1 |
if (ref($input{'pA'}) =~ /ARRAY/i) { } |
|
234
|
0 |
11 |
unless ref $input{'pC'} |
|
235
|
0 |
11 |
unless ref $input{'pG'} |
|
236
|
0 |
11 |
unless ref $input{'pT'} |
|
243
|
0 |
1 |
if ref $input{'pC'} |
|
244
|
0 |
1 |
if ref $input{'pG'} |
|
245
|
0 |
1 |
if ref $input{'pT'} |
|
255
|
1 |
6 |
if (do {
$$self{'probA'}
}->[$i] and do {
$$self{'probA'}
}->[$i] eq 'a') |
|
258
|
1 |
6 |
if (do {
$$self{'probC'}
}->[$i] and do {
$$self{'probC'}
}->[$i] eq 'a') |
|
261
|
0 |
7 |
if (do {
$$self{'probG'}
}->[$i] and do {
$$self{'probG'}
}->[$i] eq 'a') |
|
264
|
0 |
7 |
if (do {
$$self{'probT'}
}->[$i] and do {
$$self{'probT'}
}->[$i] eq 'a') |
|
272
|
0 |
267 |
if (do {
$$self{'probA'}
}->[$i] + do {
$$self{'probC'}
}->[$i] + do {
$$self{'probG'}
}->[$i] + do {
$$self{'probT'}
}->[$i] == 0) |
|
279
|
0 |
267 |
if ($self->{'correction'}) |
|
295
|
0 |
6 |
if (not defined $self->{'logA'} and $input{'model'}) |
|
315
|
0 |
12 |
if $len != $lc |
|
316
|
0 |
12 |
if $len != $lt |
|
317
|
0 |
12 |
if $len != $lg |
|
347
|
0 |
0 |
unless $model{$let} > 0 and $model{$let} < 1 |
|
373
|
0 |
104 |
unless ref $self |
|
377
|
101 |
3 |
if ($pos < $len) { } |
|
409
|
0 |
2 |
if (@_) |
|
426
|
1 |
2 |
if (@_) |
|
443
|
0 |
1 |
if (@_) |
|
461
|
0 |
0 |
if (@_) |
|
479
|
0 |
8 |
if ($thresh) |
|
520
|
0 |
0 |
if (@_) |
|
539
|
0 |
5 |
if ($thresh) |
|
580
|
68 |
199 |
if $a == $total |
|
581
|
9 |
190 |
if $g == $total |
|
582
|
82 |
108 |
if $c == $total |
|
583
|
15 |
93 |
if $t == $total |
|
585
|
0 |
93 |
if $r == $total |
|
587
|
7 |
86 |
if $y == $total |
|
589
|
24 |
62 |
if $m == $total |
|
591
|
13 |
49 |
if $k == $total |
|
593
|
7 |
42 |
if $s == $total |
|
595
|
22 |
20 |
if $w == $total |
|
597
|
3 |
17 |
if $d == $total |
|
599
|
8 |
9 |
if $v == $total |
|
601
|
2 |
7 |
if $b == $total |
|
603
|
6 |
1 |
if $h == $total |
|
631
|
23 |
43 |
if $a < $thresh and $c < $thresh and $g < $thresh and $t < $thresh |
|
632
|
0 |
48 |
if $a == $t and $a == $c and $a == $g |
|
636
|
98 |
0 |
if $a >= $thresh and $a > $t and $a > $c and $a > $g |
|
637
|
101 |
0 |
if $c >= $thresh and $c > $t and $c > $a and $c > $g |
|
638
|
19 |
0 |
if $g >= $thresh and $g > $t and $g > $c and $g > $a |
|
639
|
24 |
2 |
if $t >= $thresh and $t > $g and $t > $c and $t > $a |
|
663
|
1 |
0 |
if ($base eq 'A') |
|
664
|
0 |
0 |
if ($base eq 'C') |
|
665
|
0 |
0 |
if ($base eq 'G') |
|
666
|
0 |
0 |
if ($base eq 'T') |
|
673
|
1 |
4 |
if $next eq '10' |
|
692
|
3 |
0 |
if $base eq 'A' |
|
693
|
0 |
0 |
if $base eq 'C' |
|
694
|
0 |
0 |
if $base eq 'G' |
|
695
|
0 |
0 |
if $base eq 'T' |
|
712
|
1 |
0 |
if $base eq 'A' and $self->{'logA'} |
|
713
|
0 |
0 |
if $base eq 'C' and $self->{'logC'} |
|
714
|
0 |
0 |
if $base eq 'G' and $self->{'logG'} |
|
715
|
0 |
0 |
if $base eq 'T' and $self->{'logT'} |
|
716
|
0 |
0 |
unless grep /$base/, ('A', 'C', 'G', 'T') |
|
733
|
2 |
10 |
if (@_) |
|
754
|
1 |
4 |
if ($letter eq 'A') |
|
755
|
1 |
3 |
if ($letter eq 'C') |
|
756
|
0 |
3 |
if ($letter eq 'G') |
|
757
|
0 |
3 |
if ($letter eq 'T') |
|
758
|
0 |
3 |
if ($letter eq 'M') |
|
759
|
0 |
3 |
if ($letter eq 'R') |
|
760
|
0 |
3 |
if ($letter eq 'W') |
|
761
|
0 |
3 |
if ($letter eq 'S') |
|
762
|
0 |
3 |
if ($letter eq 'Y') |
|
763
|
0 |
3 |
if ($letter eq 'K') |
|
764
|
1 |
2 |
if ($letter eq 'V') |
|
765
|
0 |
2 |
if ($letter eq 'H') |
|
766
|
1 |
1 |
if ($letter eq 'D') |
|
767
|
1 |
0 |
if ($letter eq 'B') |
|
794
|
1 |
4 |
if ($letter eq 'A') |
|
795
|
1 |
3 |
if ($letter eq 'C') |
|
796
|
0 |
3 |
if ($letter eq 'G') |
|
797
|
0 |
3 |
if ($letter eq 'T') |
|
798
|
0 |
3 |
if ($letter eq 'M') |
|
799
|
0 |
3 |
if ($letter eq 'R') |
|
800
|
0 |
3 |
if ($letter eq 'W') |
|
801
|
0 |
3 |
if ($letter eq 'S') |
|
802
|
0 |
3 |
if ($letter eq 'Y') |
|
803
|
0 |
3 |
if ($letter eq 'K') |
|
804
|
1 |
2 |
if ($letter eq 'V') |
|
805
|
0 |
2 |
if ($letter eq 'H') |
|
806
|
1 |
1 |
if ($letter eq 'D') |
|
807
|
1 |
0 |
if ($letter eq 'B') |
|
832
|
0 |
3 |
unless $array and $lm |
|
833
|
0 |
3 |
unless $direct |
|
834
|
2 |
1 |
$direct == 1 ? : |
|
836
|
0 |
62 |
if $c > $lm |
|
837
|
0 |
62 |
if $c < -$lm and $direct != 1 |
|
838
|
0 |
62 |
if $c < 0 and $direct == 1 |
|
840
|
25 |
37 |
if $direct != 1 |
|
862
|
0 |
3 |
unless $str and $lm |
|
863
|
0 |
3 |
unless $direct |
|
864
|
2 |
1 |
$direct == 1 ? : |
|
867
|
25 |
37 |
if $direct != 1 |
|
894
|
2 |
0 |
if ($base eq 'A') |
|
895
|
2 |
0 |
if defined $self->{'probA'} |
|
898
|
0 |
0 |
if ($base eq 'G') |
|
899
|
0 |
0 |
if defined $self->{'probG'} |
|
902
|
0 |
0 |
if ($base eq 'C') |
|
903
|
0 |
0 |
if defined $self->{'probC'} |
|
906
|
0 |
0 |
if ($base eq 'T') |
|
907
|
0 |
0 |
if defined $self->{'probT'} |
|
934
|
1 |
0 |
if defined $self->{'logA'} |
|
|
1 |
0 |
if ($base eq 'A') |
|
935
|
0 |
0 |
if defined $self->{'logC'} |
|
|
0 |
0 |
if ($base eq 'C') |
|
936
|
0 |
0 |
if defined $self->{'logG'} |
|
|
0 |
0 |
if ($base eq 'G') |
|
937
|
0 |
0 |
if defined $self->{'logT'} |
|
|
0 |
0 |
if ($base eq 'T') |
|
959
|
0 |
1 |
unless $self->{'logA'} |
|
961
|
0 |
1 |
unless length $seq == @{$self->{'logA'};} |
|
968
|
0 |
25 |
unless defined $self->{$tv} |
|
969
|
25 |
0 |
defined $self->{$tv} ? : |
|
991
|
0 |
0 |
if $thresh < 0 or $thresh > 1 |
|
995
|
0 |
0 |
if $self->{'probA'}[$i] > $thresh |
|
996
|
0 |
0 |
if $self->{'probC'}[$i] > $thresh |
|
997
|
0 |
0 |
if $self->{'probG'}[$i] > $thresh |
|
998
|
0 |
0 |
if $self->{'probT'}[$i] > $thresh |
|
999
|
0 |
0 |
if $seq[$i] eq 'N' |