| line |
true |
false |
branch |
|
124
|
0 |
2 |
if ($file =~ /^STDIN$/i) { } |
|
|
2 |
0 |
elsif (ref $file eq '' or ref $file eq 'SCALAR') { } |
|
128
|
0 |
2 |
unless open $fh, '<', $file |
|
137
|
2 |
0 |
if $_ eq '>' |
|
140
|
0 |
6 |
if $finished |
|
145
|
2 |
2 |
if substr($_, -1, 1) eq '>' |
|
157
|
0 |
4 |
if substr($head, -1, 1) eq "\r" |
|
159
|
4 |
0 |
if (length $head > 0) |
|
163
|
4 |
0 |
unless $not_trim |
|
168
|
2 |
0 |
if $open_flg |
|
182
|
0 |
0 |
if ($file =~ /^STDIN$/i) { } |
|
186
|
0 |
0 |
unless open $fh, '<', $file |
|
190
|
0 |
0 |
if $finished |
|
195
|
0 |
0 |
if (/^>(.*)/) { } |
|
200
|
0 |
0 |
if ($header ne '') |
|
201
|
0 |
0 |
unless $not_trim |
|
209
|
0 |
0 |
unless $is_stdin |
|
213
|
0 |
0 |
if ($last_header ne '') |
|
214
|
0 |
0 |
unless $not_trim |
|
260
|
0 |
1 |
unless (ref $seqs eq 'HASH') |
|
264
|
1 |
0 |
unless defined $n |
|
266
|
0 |
1 |
unless open my $fh2, ">$file" |
|
285
|
0 |
2 |
unless defined $n |
|
286
|
0 |
2 |
unless ($n =~ /^\d+$/ and $n > 0) |
|
321
|
1 |
1 |
if $seq =~ /[^\.\-\s_*ABCDEFGHIKLMNPQRSTUVWY]/i |
|
389
|
0 |
1 |
if ($seq eq '') |
|
424
|
0 |
0 |
exists $bases{$_} ? : |
|
544
|
0 |
0 |
if (exists $genetic_code{$codon}) { } |
|
564
|
0 |
0 |
unless (ref $alphabet eq 'ARRAY') |
|
588
|
0 |
0 |
unless defined $file_out |
|
589
|
0 |
0 |
unless open my $fh2, ">$file_out" |
|
611
|
0 |
0 |
unless open my $fh, '<', $file |
|
612
|
0 |
0 |
unless open my $fh2, '>', $outfile |
|
617
|
0 |
0 |
if (/^\s*>(.*)\r?\n/) { } |
|
619
|
0 |
0 |
if ($head =~ /$regex/) |
|
652
|
0 |
0 |
unless defined $replacement |
|
655
|
0 |
0 |
unless defined $symbols |
|
656
|
0 |
0 |
unless (ref $symbols eq 'ARRAY') |
|
661
|
0 |
0 |
unless open my $fh, '<', $file |
|
662
|
0 |
0 |
unless open my $fh2, '>', $outfile |
|
667
|
0 |
0 |
if (/^\s*>(.*)\r?\n/) { } |
|
669
|
0 |
0 |
if ($head =~ /[$re]/) |