| line |
true |
false |
branch |
|
48
|
1 |
141 |
if (@_ and @_ > 0 and $_[-1] and exists $STRAND_CHAR_TABLE{$_[-1]}) { }
|
|
59
|
0 |
0 |
if (-f $f . '.fai') { }
|
|
|
0 |
0 |
elsif (-f $f . '.nhr') { }
|
|
|
0 |
0 |
elsif ($SAMTOOLS_CMD) { }
|
|
62
|
0 |
0 |
unless open my $fh, '-|', $BLASTDB_CMD, '-db', $f, '-entry', 'all', '-outfmt', "%a\t%l"
|
|
67
|
0 |
0 |
unless system('samtools', 'faidx', $f) == 0
|
|
68
|
0 |
0 |
if -f $f . '.fai'
|
|
72
|
0 |
0 |
unless ($d)
|
|
84
|
0 |
0 |
if $sl{$r->[0]}
|
|
98
|
0 |
0 |
unless ref $sub eq 'CODE' and -f $f
|
|
104
|
0 |
0 |
if ($pattern)
|
|
133
|
0 |
0 |
if &blessed($seq1)
|
|
134
|
0 |
0 |
if &blessed($seq2)
|
|
138
|
0 |
0 |
unless ($include_gaps)
|
|
148
|
0 |
0 |
if (length($seq2) - $seq2_gaps < length($seq1) - $seq1_gaps) { }
|
|
156
|
0 |
0 |
if ($use_longest) { }
|
|
208
|
0 |
0 |
unless defined $pattern
|
|
211
|
0 |
0 |
if (ref $pattern eq 'CODE') { }
|
|
|
0 |
0 |
elsif (ref $pattern eq 'HASH') { }
|
|
217
|
0 |
0 |
defined $pattern->{$id} ? :
|
|
229
|
0 |
0 |
unless $seq
|
|
230
|
0 |
0 |
unless (&blessed($seq))
|
|
231
|
0 |
0 |
if (ref $seq eq 'ARRAY') { }
|
|
256
|
1 |
24 |
unless ($initialized)
|
|
264
|
0 |
2048 |
if $parth & 1
|
|
266
|
1024 |
1024 |
if $rflag
|
|
281
|
0 |
25 |
wantarray ? :
|