| line |
!l |
l&&!r |
l&&r |
condition |
|
331
|
0 |
0 |
0 |
$self->_validate_file_input(-'ind', $self->io->catfile(dirname($self->executable), 'indexes', $index)) and $index = $self->io->catfile(dirname($self->executable), 'indexes', $index) |
|
|
0 |
0 |
0 |
$self->_validate_file_input(-'ind', $self->io->catfile($ENV{'BOWTIE_INDEXES'}, $index)) and $index = $self->io->catfile($ENV{'BOWTIE_INDEXES'}, $index) |
|
409
|
0 |
0 |
0 |
$self->_validate_file_input(-'ind', $self->io->catfile(dirname($self->executable), 'indexes', $index)) and $index = $self->io->catfile(dirname($self->executable), 'indexes', $index) |
|
|
0 |
0 |
0 |
$self->_validate_file_input(-'ind', $self->io->catfile($ENV{'BOWTIE_INDEXES'}, $index)) and $index = $self->io->catfile($ENV{'BOWTIE_INDEXES'}, $index) |
|
469
|
0 |
0 |
0 |
defined $want and $want eq 'format' |
|
477
|
0 |
0 |
0 |
/^bowtie/i and $want =~ /^Bio::Assembly::Scaffold/ |
|
478
|
0 |
0 |
0 |
defined $self->{'_result'}{'object'} and ref($self->{'_result'}{'object'}) =~ /^Bio::Assembly::Scaffold/ |
|
487
|
0 |
0 |
0 |
/^bowtie/i and $want =~ /^Bio::SeqFeature::Collection/ |
|
491
|
0 |
0 |
0 |
/^sam/i and $want =~ /^Bio::Assembly::Scaffold/ |
|
492
|
0 |
0 |
0 |
defined $self->{'_result'}{'object'} and ref($self->{'_result'}{'object'}) =~ /^Bio::Assembly::Scaffold/ |
|
502
|
0 |
0 |
0 |
/^sam/i and $want =~ /^Bio::SeqFeature::Collection/ |
|
503
|
0 |
0 |
0 |
defined $self->{'_result'}{'object'} and ref($self->{'_result'}{'object'}) =~ /^Bio::Assembly::Scaffold/ |
|
523
|
0 |
0 |
0 |
/^Bio::SeqIO/ and $format eq 'fasta' |
|
524
|
0 |
0 |
0 |
defined $self->{'_result'}{'object'} and ref($self->{'_result'}{'object'}) =~ /^Bio::SeqIO/ |
|
532
|
0 |
0 |
0 |
/^Bio::SeqIO/ and $format ne 'fasta' |
|
592
|
0 |
0 |
0 |
-e $file and -r _ |
|
642
|
0 |
0 |
0 |
-e $args{$_} and -r _ |
|
649
|
0 |
0 |
0 |
-e $args{$_} . '.1.ebwt' and -e $args{$_} . '.2.ebwt' |
|
|
0 |
0 |
0 |
-e $args{$_} . '.1.ebwt' and -e $args{$_} . '.2.ebwt' and -e $args{$_} . '.3.ebwt' |
|
|
0 |
0 |
0 |
-e $args{$_} . '.1.ebwt' and -e $args{$_} . '.2.ebwt' and -e $args{$_} . '.3.ebwt' and -e $args{$_} . '.4.ebwt' |
|
|
0 |
0 |
0 |
-e $args{$_} . '.1.ebwt' and -e $args{$_} . '.2.ebwt' and -e $args{$_} . '.3.ebwt' and -e $args{$_} . '.4.ebwt' and -e $args{$_} . '.rev.1.ebwt' |
|
|
0 |
0 |
0 |
-e $args{$_} . '.1.ebwt' and -e $args{$_} . '.2.ebwt' and -e $args{$_} . '.3.ebwt' and -e $args{$_} . '.4.ebwt' and -e $args{$_} . '.rev.1.ebwt' and -e $args{$_} . '.rev.2.ebwt' |
|
716
|
0 |
0 |
0 |
UNIVERSAL::isa($read, 'can') and $read->isa('Bio::PrimarySeqI') |