Condition Coverage

blib/lib/Bio/Tools/Run/Bowtie.pm
Criterion Covered Total %
condition 0 129 0.0


and 3 conditions

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')

or 3 conditions

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