| line |
true |
false |
branch |
|
26
|
9 |
64 |
if (defined $_[0] and substr($_[0], 0, 1) eq '-') { } |
|
30
|
8 |
5 |
if ($i =~ /^-(file|filename)/iu) { } |
|
|
4 |
1 |
elsif ($i =~ /^-(loadseqs)/iu) { } |
|
45
|
6 |
66 |
if (defined $args->{'loadseqs'}) |
|
46
|
4 |
2 |
if ($args->{'loadseqs'} eq 'name' or $args->{'loadseqs'} eq 'names') { } |
|
|
1 |
1 |
elsif ($args->{'loadseqs'} eq 'seq' or $args->{'loadseqs'} eq 'seqs' or $args->{'loadseqs'} eq '1') { } |
|
|
1 |
0 |
elsif ($args->{'loadseqs'} eq 'records') { } |
|
67
|
0 |
72 |
if (defined $self->{'filename'} and -d $self->{'filename'}) |
|
71
|
70 |
2 |
if (defined $self->{'filename'} and $self->{'filename'} ne '{{STDIN}}') { } |
|
72
|
4 |
66 |
unless open my $initial_fh, "<", $self->{'filename'} |
|
77
|
33 |
33 |
if (substr($magic_byte, 0, 3) eq "\037\213\cH") { } |
|
|
0 |
33 |
elsif (-B $self->{'filename'}) { } |
|
81
|
0 |
33 |
if (not defined $GZIP_BIN) { } |
|
88
|
0 |
33 |
unless open my $fh, "-|", "$GZIP_BIN -dc $self->{'filename'}" |
|
101
|
0 |
33 |
unless open my $fh, "<:encoding(utf8):crlf", $self->{'filename'} |
|
109
|
0 |
2 |
if ($self->{'loadseqs'}) |
|
117
|
6 |
62 |
if ($self->{'loadseqs'}) |
|
128
|
0 |
1 |
unless $self->{'loadseqs'} eq "records" |
|
139
|
0 |
181 |
if defined $self->{'status'} and $self->{'status'} == 0 |
|
143
|
0 |
181 |
unless @{$self->{'aux'};} |
|
146
|
15 |
166 |
if ($self->{'aux'}[1]) |
|
150
|
117 |
64 |
unless (defined $self->{'aux'}[0]) |
|
154
|
95 |
6 |
if (substr($self->{'line'}, 0, 1) eq ">" or substr($self->{'line'}, 0, 1) eq "\@") |
|
159
|
22 |
95 |
unless (defined $self->{'aux'}[0]) |
|
168
|
0 |
159 |
unless defined $self->{'line'} |
|
170
|
88 |
0 |
$self->{'line'} =~ /^.(\S+)/u ? : |
|
|
71 |
88 |
$self->{'line'} =~ /^.(\S+)(?:\s+)(.+)/u ? : |
|
178
|
65 |
220 |
if $c eq ">" or $c eq "\@" or $c eq "+" |
|
182
|
18 |
141 |
unless defined $self->{'aux'}[0] |
|
188
|
94 |
65 |
if ($c ne "+") |
|
199
|
65 |
0 |
if (length $qual >= length $seq) |
|
228
|
5 |
42 |
unless defined $scalar_read |
|
241
|
0 |
7 |
if defined $self->{'status'} and $self->{'status'} == 0 |
|
252
|
1 |
6 |
unless (defined $qual) |
|
253
|
0 |
1 |
if (defined $header) |
|
261
|
5 |
1 |
if (substr($header, 0, 1) eq '@' and substr($check, 0, 1) eq '+') { } |
|
266
|
4 |
1 |
if ($seq =~ /^[ACGTNacgtn]+$/u and length $seq == length $qual) { } |
|
284
|
1 |
0 |
if (substr($header, 0, 1) eq ">") |
|
299
|
0 |
16 |
if defined $self->{'status'} and $self->{'status'} == 0 |
|
310
|
2 |
14 |
unless (defined $qual) |
|
311
|
0 |
2 |
if (defined $header) |
|
319
|
14 |
0 |
if (substr($header, 0, 1) eq '@' and substr($check, 0, 1) eq '+') { } |
|
324
|
14 |
0 |
if ($seq =~ /^[ACGTNacgtn]+$/u and length $seq == length $qual) { } |
|
330
|
0 |
14 |
unless (defined $y) |
|
352
|
7 |
7 |
if (defined $comments) |
|
354
|
7 |
0 |
if (defined $ctrl) |
|
356
|
7 |
0 |
$filtered eq 'N' ? : |
|
358
|
7 |
0 |
if ($read eq '1') { } |
|
379
|
0 |
0 |
if (substr($header, 0, 1) eq ">") |
|
392
|
0 |
4 |
unless defined $filename |
|
394
|
0 |
4 |
unless open my $fh, "<", $filename |
|
398
|
0 |
4 |
if (substr($magic_byte, 0, 3) eq "\037\213\cH") { } |
|
400
|
0 |
0 |
if (not defined $self->{'GZIP_BIN'}) { } |
|
404
|
0 |
0 |
unless open $fh, "-|", "$self->{'GZIP_BIN'} -dc $filename" |
|
411
|
1 |
3 |
if (substr($first, 0, 1) eq '>') { } |
|
|
2 |
1 |
elsif (substr($first, 0, 1) eq '@') { } |
|
418
|
2 |
0 |
if (substr($sep, 0, 1) eq "+") |
|
429
|
0 |
6 |
unless defined $self->{'loadseqs'} |
|
434
|
12 |
10 |
if ($self->{'loadseqs'} eq 'name') { } |
|
|
3 |
7 |
elsif ($self->{'loadseqs'} eq 'seq') { } |
|
454
|
0 |
33 |
if $^O eq "MSWin32" |
|
456
|
33 |
0 |
if ($has_which) { } |
|
458
|
33 |
33 |
if which($cmd) |
|
467
|
0 |
0 |
if $exit == 0 and not $@ |