| line |
true |
false |
branch |
|
182
|
0 |
6 |
unless $Bio::Tools::Lucy::OK_FIELD{$attr} |
|
183
|
4 |
2 |
if @_ |
|
261
|
0 |
1 |
if $self->{'lucy_verbose'} |
|
262
|
0 |
1 |
unless open my $SEQ, '<', $self->{'seqfile'} |
|
268
|
1 |
22 |
if ($line =~ /^>(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)/) { } |
|
270
|
0 |
1 |
if ($self->{'fwd_desig'}) |
|
271
|
0 |
0 |
if $name =~ /^(\S+)($self->{'fwd_desig'})$/ |
|
273
|
1 |
0 |
if ($self->{'rev_desig'}) |
|
274
|
1 |
0 |
if $name =~ /^(\S+)($self->{'rev_desig'})$/ |
|
295
|
0 |
1 |
if ($self->{'qualfile'}) { } |
|
|
1 |
0 |
elsif (-e "$file.qual") { } |
|
296
|
0 |
0 |
unless open my $QUAL, '<', $self->{'qualfile'} |
|
300
|
0 |
1 |
if $self->{'lucy_verbose'} |
|
302
|
0 |
1 |
unless open my $QUAL, '<', "$file.qual" |
|
306
|
0 |
0 |
if $self->{'lucy_verbose'} |
|
314
|
1 |
54 |
if ($line =~ /^>(\S+)/) { } |
|
334
|
0 |
1 |
if ($self->{'infofile'}) { } |
|
|
1 |
0 |
elsif (-e "$file.info") { } |
|
335
|
0 |
0 |
unless open my $INFO, '<', $self->{'infofile'} |
|
339
|
0 |
1 |
if $self->{'lucy_verbose'} |
|
341
|
0 |
1 |
unless open my $INFO, '<', "$file.info" |
|
345
|
0 |
0 |
if $self->{'lucy_verbose'} |
|
351
|
1 |
0 |
if ($2 > 0 and $3 > 0) |
|
352
|
1 |
0 |
if $self->{'sequences'}{$1} |
|
358
|
0 |
1 |
if ($self->{'stderrfile'}) { } |
|
|
1 |
0 |
elsif (-e "$file.stderr") { } |
|
359
|
0 |
0 |
unless open my $STDERR_LUCY, '<', $self->{'stderrfile'} |
|
363
|
0 |
1 |
if $self->{'lucy_verbose'} |
|
365
|
0 |
1 |
unless open my $STDERR_LUCY, '<', "$file.stderr" |
|
369
|
0 |
0 |
if $self->{'lucy_verbose'} |
|
373
|
1 |
0 |
if ($self->{'adv_stderr'}) { } |
|
375
|
1 |
1 |
if /dropping\s+(\S+)/ |
|
376
|
0 |
2 |
if /Vector: (\S+)/ |
|
377
|
0 |
2 |
if /Empty: (\S+)/ |
|
378
|
0 |
2 |
if m[Short/ no insert: (\S+)] |
|
379
|
1 |
1 |
if /(\S+) has PolyA/ |
|
380
|
0 |
2 |
if (/Dropped PolyA: (\S+)/) |
|
388
|
0 |
0 |
if /dropping\s+(\S+)/ |
|
513
|
1 |
0 |
if $self->{'sequences'}{$key}{'direction'} |
|
613
|
1 |
0 |
if $self->{'sequences'}{$key}{'full_length'} |
|
633
|
1 |
0 |
if $self->{'sequences'}{$key}{'polyA'} |