| line |
true |
false |
branch |
|
98
|
17 |
54 |
if $val |
|
115
|
5 |
36 |
if $val |
|
135
|
0 |
0 |
if (defined $val) { } |
|
138
|
0 |
0 |
unless (defined $self->{'_out_type'}) |
|
158
|
9 |
0 |
if (defined $asm_format) |
|
178
|
1 |
0 |
if (defined $asm_variant) |
|
197
|
0 |
0 |
unless (defined $self->executable) |
|
219
|
0 |
0 |
if (not $seqs) { } |
|
223
|
0 |
0 |
if (ref($seqs) =~ /ARRAY/i) { } |
|
225
|
0 |
0 |
unless ($seq->isa('Bio::PrimarySeqI') or $seq->isa('Bio::SeqI')) |
|
230
|
0 |
0 |
unless (-f $seqs) |
|
252
|
0 |
0 |
if (defined $quals) |
|
253
|
0 |
0 |
if (ref($quals) =~ /ARRAY/i) { } |
|
255
|
0 |
0 |
unless ($qual->isa('Bio::Seq::QualI') or $qual->isa('Bio::Seq::Quality')) |
|
260
|
0 |
0 |
unless (-f $quals) |
|
294
|
0 |
0 |
if (ref($seqs) =~ /ARRAY/i) { } |
|
296
|
0 |
0 |
if (defined $quals and not ref($quals) =~ /ARRAY/i) { } |
|
307
|
0 |
0 |
if (defined $quals and ref($quals) =~ /ARRAY/i) { } |
|
345
|
0 |
0 |
unless (defined $seq->id) |
|
354
|
0 |
0 |
if ($seq->isa('Bio::Seq::Quality')) { } |
|
356
|
0 |
0 |
if (scalar @{$seq->qual;} > 0) |
|
363
|
0 |
0 |
if (defined $qual) |
|
365
|
0 |
0 |
if ($qualid eq $seqid) { } |
|
381
|
0 |
0 |
if scalar @$seqs <= 0 |
|
382
|
0 |
0 |
if $use_qual_file == 0 |
|
402
|
0 |
0 |
if (not $out_type eq 'Bio::Assembly::ScaffoldI' || $out_type eq 'Bio::Assembly::IO') { } |
|
406
|
0 |
0 |
unless open $output_fh, '>', $output_file |
|
436
|
0 |
0 |
if (not $out_type eq 'Bio::Assembly::ScaffoldI' || $out_type eq 'Bio::Assembly::IO') { } |
|
448
|
0 |
0 |
unless $keep_asm |
|
449
|
0 |
0 |
if ($out_type eq 'Bio::Assembly::IO') { } |
|
455
|
0 |
0 |
if ($out_type eq 'Bio::Assembly::ScaffoldI') { } |
|
519
|
2 |
9 |
if ($cmd) |
|
521
|
0 |
2 |
unless $self->{'_options'}{'_commands'} |
|
522
|
0 |
2 |
unless grep /^$cmd$/, @{$$self{'_options'}{'_commands'};} |
|
523
|
2 |
0 |
if ($self->{'_options'}{'_prefixes'}) |
|
529
|
2 |
0 |
$cmd ? : |
|
530
|
2 |
0 |
$cmd ? : |
|
534
|
2 |
0 |
$cmd ? : |
|
544
|
0 |
11 |
if (not defined $use_dash) { } |
|
549
|
0 |
11 |
if (not defined $join) { } |
|
598
|
1 |
0 |
if ($_ == 1) |
|
602
|
0 |
0 |
if (/^s/) |
|
606
|
0 |
0 |
if (/^d/) |
|
610
|
0 |
0 |
if (/^m/) |
|
631
|
11 |
1 |
if (defined $name) { } |
|
632
|
1 |
10 |
if ($name =~ /command/i) { } |
|
|
3 |
7 |
elsif (defined $translat->{$name}) { } |
|
652
|
0 |
1 |
if ($dash =~ /^m/) |
|
719
|
0 |
0 |
if defined $self->$opt |
|
756
|
0 |
0 |
if (defined $qual_param) |
|
757
|
0 |
0 |
if ($qual_file) { } |
|
835
|
6 |
1 |
unless (exists $reset_args{"-$p"}) |
|
840
|
2 |
0 |
unless (exists $reset_args{"-$s"}) |
|
865
|
260 |
5 |
if @_ |
|
887
|
1 |
2 |
if (not defined $_ or /^a/) |
|
891
|
1 |
1 |
if (/^p/i) |
|
895
|
1 |
0 |
if (/^s/i) |
|
924
|
0 |
1 |
if (/^p/i) |
|
926
|
0 |
0 |
if $self->can($_) and defined $self->$_ |
|
930
|
0 |
1 |
if (/^s/i) |
|
932
|
0 |
0 |
if $self->can($_) and defined $self->$_ |
|
936
|
1 |
0 |
if (/^a/i) |
|
938
|
4 |
5 |
if $self->can($_) and defined $self->$_ |