| 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, $err) |
|
862
|
0 |
0 |
if ($@) |