| line |
true |
false |
branch |
|
137
|
0 |
48 |
if ($sbjct->num_hsps == 0) { } |
|
|
38 |
10 |
elsif ($sbjct->num_hsps == 1) { } |
|
188
|
0 |
53 |
unless defined $frame |
|
213
|
43 |
10 |
if (defined $start_stop{'qstart'}) { } |
|
220
|
5 |
38 |
$qstart < $start_stop{'qstart'} ? : |
|
222
|
20 |
23 |
$qstop > $start_stop{'qstop'} ? : |
|
224
|
9 |
34 |
$sstart < $start_stop{'sstart'} ? : |
|
226
|
13 |
30 |
$sstop > $start_stop{'sstop'} ? : |
|
250
|
0 |
21 |
if ($v > 0) |
|
300
|
7 |
3 |
if ($qoverlap) { } |
|
|
2 |
1 |
elsif ($soverlap) { } |
|
301
|
5 |
2 |
if ($soverlap) { } |
|
355
|
0 |
128 |
if ($algo =~ /^(?:PSI)?T(?:BLASTN|FAST(?:X|Y|XY))/io) { } |
|
|
4 |
124 |
elsif ($algo =~ /^(?:BLASTX|FAST(?:X|Y|XY))/io) { } |
|
|
40 |
84 |
elsif ($algo =~ /^TBLASTX/io) { } |
|
356
|
0 |
0 |
if $type =~ /sbjct|hit|tot/i |
|
358
|
2 |
2 |
if $type =~ /query|tot/i |
|
395
|
22 |
189 |
unless $_->{'frame'} == $frame and $_->{'strand'} == $strand |
|
398
|
18 |
171 |
if ($start >= $_->{'start'} and $stop <= $_->{'stop'}) |
|
404
|
12 |
159 |
if ($start < $_->{'start'} and $stop >= $_->{'start'} + $max_overlap - 1) |
|
409
|
0 |
12 |
if ($numID eq '') |
|
413
|
0 |
12 |
if ($numCons eq '') |
|
418
|
0 |
12 |
if ($@) { } |
|
429
|
17 |
154 |
if ($stop > $_->{'stop'} and $start <= $_->{'stop'} - $max_overlap + 1) |
|
434
|
0 |
17 |
if ($numID eq '') |
|
438
|
0 |
17 |
if ($numCons eq '') |
|
443
|
0 |
17 |
if ($@) { } |
|
453
|
29 |
142 |
if $overlap |
|
456
|
20 |
86 |
if ($overlap and @$contigs_ref > 1) { } |
|
|
62 |
24 |
elsif (not $overlap) { } |
|
460
|
6 |
44 |
unless do {
$contigs_ref
}->[$i] |
|
464
|
3 |
52 |
unless do {
$contigs_ref
}->[$u] |
|
467
|
2 |
50 |
if ($u_start < $i_start and $u_stop >= $i_start + $max_overlap - 1) { } |
|
|
3 |
47 |
elsif ($u_stop > $i_stop and $u_start <= $i_stop - $max_overlap + 1) { } |
|
|
1 |
65 |
elsif ($u_start >= $i_start and $u_stop <= $i_stop) { } |
|
474
|
0 |
4 |
unless $hsp_start < $use_start |
|
479
|
0 |
4 |
if ($these_ids eq '') |
|
483
|
0 |
4 |
if ($these_cons eq '') |
|
488
|
0 |
4 |
if ($@) { } |
|
494
|
2 |
2 |
if $hsp_start == $u_start |
|
511
|
0 |
4 |
unless $hsp_end > $use_stop |
|
516
|
0 |
4 |
if ($these_ids eq '') |
|
520
|
0 |
4 |
if ($these_cons eq '') |
|
525
|
0 |
4 |
if ($@) { } |
|
531
|
3 |
1 |
if $hsp_end == $u_stop |
|
559
|
0 |
62 |
if ($numID eq '') |
|
563
|
0 |
62 |
if ($numCons eq '') |
|
599
|
0 |
0 |
if (defined $exp) { } |
|
|
0 |
0 |
elsif ($num == 0) { } |
|
|
0 |
0 |
elsif (not $num =~ /\./) { } |
|
600
|
0 |
0 |
unless $num |
|
601
|
0 |
0 |
if $num >= 5 |
|
602
|
0 |
0 |
if $num <= -5 |
|
609
|
0 |
0 |
if $num =~ /\.$/ |
|
612
|
0 |
0 |
unless ($num =~ /^0/) |
|
617
|
0 |
0 |
if $c == 0 |
|
620
|
0 |
0 |
if $num == 0 and not $rev |
|
621
|
0 |
0 |
if $rev |
|
650
|
47 |
6465 |
unless ($from) |
|
652
|
175 |
6290 |
if $a[$i] == $a[$i - 1] |
|
653
|
4436 |
1854 |
if ($a[$i] == $a[$i - 1] + 1) { } |
|
657
|
290 |
1564 |
if ($consec == 1) { } |
|
658
|
757 |
807 |
$consec > 1 ? : |
|
665
|
23 |
27 |
if (defined $to) |
|
666
|
3 |
20 |
if ($consec == 1) { } |
|
667
|
20 |
0 |
$consec > 1 ? : |
|
669
|
47 |
3 |
if $from |
|
719
|
0 |
0 |
unless ref $string_ref eq 'SCALAR' |
|
728
|
0 |
0 |
if $str =~ s/(\A|\n)]+> ?/>/sig |
|
731
|
0 |
0 |
if $str =~ s/<[^>]+>| //sig |
|
734
|
0 |
0 |
if $str =~ s/(\A|\n)>\s+/\n\n>/sig |