| 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') |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
305
|
0 |
0 |
0 |
$seq ||= $arg1 |
|
306
|
0 |
0 |
0 |
$index ||= $arg2 |
|
307
|
0 |
0 |
0 |
$seq2 ||= $arg3 |
|
331
|
0 |
0 |
0 |
$self->_validate_file_input('-ind', $index) or $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', $index) or $self->_validate_file_input('-ind', $self->io->catfile(dirname($self->executable), 'indexes', $index)) and $index = $self->io->catfile(dirname($self->executable), 'indexes', $index) or $self->_validate_file_input('-ind', $self->io->catfile($ENV{'BOWTIE_INDEXES'}, $index)) and $index = $self->io->catfile($ENV{'BOWTIE_INDEXES'}, $index) |
|
369
|
0 |
0 |
0 |
$ref ||= $arg1 |
|
370
|
0 |
0 |
0 |
$index ||= $arg2 |
|
372
|
0 |
0 |
0 |
$index ||= $self->io->tempdir('CLEANUP', 1) . '/index' |
|
401
|
0 |
0 |
0 |
$index ||= $arg1 |
|
402
|
0 |
0 |
0 |
$out ||= $arg2 |
|
409
|
0 |
0 |
0 |
$self->_validate_file_input('-ind', $index) or $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', $index) or $self->_validate_file_input('-ind', $self->io->catfile(dirname($self->executable), 'indexes', $index)) and $index = $self->io->catfile(dirname($self->executable), 'indexes', $index) or $self->_validate_file_input('-ind', $self->io->catfile($ENV{'BOWTIE_INDEXES'}, $index)) and $index = $self->io->catfile($ENV{'BOWTIE_INDEXES'}, $index) |
|
470
|
0 |
0 |
0 |
not $want or $want eq 'raw' |
|
|
0 |
0 |
0 |
not $want or $want eq 'raw' or $cmd eq 'build' |
|
749
|
0 |
0 |
0 |
$cmd =~ /^c/ or $self->fastq |
|
|
0 |
0 |
0 |
$cmd =~ /^c/ or $self->fastq or $self->raw |
|
754
|
0 |
0 |
0 |
$cmd =~ /^[cb]/ or $self->fasta |
|
|
0 |
0 |
0 |
$cmd =~ /^[cb]/ or $self->fasta or $self->raw |
|
763
|
0 |
0 |
0 |
$cmd =~ /^[cb]/ or $self->fasta |
|
|
0 |
0 |
0 |
$cmd =~ /^[cb]/ or $self->fasta or $self->fastq |