Branch Coverage

blib/lib/Bio/Tools/Run/Bowtie.pm
Criterion Covered Total %
branch 16 192 8.3


line true false branch
228 0 2 unless (grep /command/, @args)
233 2 0 if ($args{'-command'} =~ /(?:single|paired|crossbow)/)
234 2 0 unless (grep /(?:sam_format|concise|quiet|refout|refidx)/, @args)
281 0 0 if (not @_ % 2) { }
283 0 0 if (grep(/^-\w+/, keys %args) == keys %args) { }
0 0 elsif (grep /^-\w+/, keys %args) { }
292 0 0 if (grep /^-\w+/, @_) { }
301 0 0 if $self->can('command')
304 0 0 if (/(?:single|paired|crossbow)/)
308 0 0 unless $seq
309 0 0 unless $index
313 0 0 unless $_
314 0 0 if (/\.gz[^.]*$/)
315 0 0 unless ($HAVE_IO_UNCOMPRESS)
331 0 0 unless $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'}, $index)
336 0 0 if ($cmd =~ /^p/) { }
337 0 0 if $seq2
339 0 0 if $seq2
346 0 0 if ($out) { }
356 0 0 unless defined $params{$_}
368 0 0 if (/build/)
371 0 0 unless $ref
373 0 0 if $arg3
378 0 0 if ($ref =~ /\.gz[^.]*$/)
379 0 0 unless ($HAVE_IO_UNCOMPRESS)
400 0 0 if (/inspect/)
403 0 0 unless $index
409 0 0 unless $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)
411 0 0 if $arg3
417 0 0 if ($out) { }
448 2 0 if @_
465 0 0 $self->want ? :
466 0 0 if $self->can('command')
469 0 0 if defined $want and $want eq 'format'
470 0 0 if not $want or $want eq 'raw' or $cmd eq 'build'
471 0 0 if $want =~ /^Bio::Root::IO/
474 0 0 if (/(?:single|paired|crossbow)/)
477 0 0 if (/^bowtie/i and $want =~ /^Bio::Assembly::Scaffold/)
478 0 0 unless (defined $self->{'_result'}{'object'} and ref($self->{'_result'}{'object'}) =~ /^Bio::Assembly::Scaffold/)
487 0 0 if (/^bowtie/i and $want =~ /^Bio::SeqFeature::Collection/)
491 0 0 if (/^sam/i and $want =~ /^Bio::Assembly::Scaffold/)
492 0 0 unless (defined $self->{'_result'}{'object'} and ref($self->{'_result'}{'object'}) =~ /^Bio::Assembly::Scaffold/)
502 0 0 if (/^sam/i and $want =~ /^Bio::SeqFeature::Collection/)
503 0 0 unless (defined $self->{'_result'}{'object'} and ref($self->{'_result'}{'object'}) =~ /^Bio::Assembly::Scaffold/)
521 0 0 if (/inspect/)
523 0 0 if (/^Bio::SeqIO/ and $format eq 'fasta')
524 0 0 unless (defined $self->{'_result'}{'object'} and ref($self->{'_result'}{'object'}) =~ /^Bio::SeqIO/)
532 0 0 if (/^Bio::SeqIO/ and $format ne 'fasta')
560 2 0 if $self->can('command')
562 0 2 if (/build/)
565 0 2 if (/inspect/)
566 0 0 if $self->{'_summary'}
567 0 0 $self->{'_names_only'} ? :
569 2 0 if (/(?:single|paired|crossbow)/)
572 2 8 if $$self{'_' . $_}
592 0 0 unless -e $file and -r _
605 0 0 if ($sort) { }
632 0 0 if (grep /^-/, @args) { }
633 0 0 if @args > 2
641 0 0 if (/^seq|seq2|ref$/)
642 0 0 unless -e $args{$_} and -r _
644 0 0 if grep {$guesser->guess =~ /$_/;} @{$Bio::Tools::Run::Bowtie::accepted_types{$_};}
646 0 0 if (/^ind$/)
649 0 0 if -e $args{$_} . '.1.ebwt' and -e $args{$_} . '.2.ebwt' and -e $args{$_} . '.3.ebwt' and -e $args{$_} . '.4.ebwt' and -e $args{$_} . '.rev.1.ebwt' and -e $args{$_} . '.rev.2.ebwt'
705 0 0 if (grep /^-/, @args) { }
706 0 0 if @args % 2
715 0 0 if ($self->inline) { }
716 0 0 if (UNIVERSAL::isa($read, 'can') and $read->isa('Bio::PrimarySeqI')) { }
719 0 0 if (ref($read) =~ /ARRAY/i) { }
722 0 0 if ($seq->isa('Bio::PrimarySeqI')) { }
725 0 0 if $read =~ /[[^:alpha:]]/
729 0 0 unless @ts
730 0 0 if (@ts > 1) { }
736 0 0 if $read =~ /[[^:alpha:]]/
741 0 0 ref($read) =~ /ARRAY/i ? :
743 0 0 if (-e $file) { }
744 0 0 if $self->can('command')
747 0 0 if (/^fasta$/)
748 0 0 if $cmd =~ /^b/
749 0 0 if $cmd =~ /^c/ or $self->fastq or $self->raw
753 0 0 if (/^fastq$/)
754 0 0 if $cmd =~ /^[cb]/ or $self->fasta or $self->raw
758 0 0 if (/^tab$/)
759 0 0 unless $cmd =~ /^c/
762 0 0 if (/^raw$/)
763 0 0 if $cmd =~ /^[cb]/ or $self->fasta or $self->fastq
775 0 0 if (@ts > 1) { }
804 0 8 if @args % 2
813 0 66 if grep /$conflict/, @added
815 6 60 if $$self{'_' . $conflict}
819 0 12 if grep /$requirement/, @removed
820 0 12 if $args{$_}
840 0 0 if $self->can('command')
842 0 0 unless defined $cmd
859 0 0 unless IPC::Run::run(\@ipc_args, $in, $out, $err)
862 0 0 if ($@)