Branch Coverage

blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm
Criterion Covered Total %
branch 73 208 35.1


line true false branch
467 12 32 if (/\@/)
468 16 28 if (/\%/)
476 4 0 if ($composite_commands)
489 0 4 if (not defined $use_dash) { }
494 0 4 if (not defined $join) { }
499 3 1 if ($name =~ /^\*/)
503 4 0 unless defined $self->program_name
504 4 0 unless defined $self->program_dir
522 4 6 if $val
538 0 32 if $val
601 1 1 if ($_ eq '1')
605 0 1 if (/^s/)
609 0 1 if (/^d/)
613 1 0 if (/^m/)
637 8 16 if (/^-/) { }
0 16 elsif (s/^"//) { }
0 16 elsif (s/"$//) { }
641 0 0 unless s/["']$//
649 0 16 $in_quotes ? :
653 0 2 if $in_quotes
656 19 0 if (defined $name) { }
657 2 17 if ($name =~ /command/i) { }
6 11 elsif (defined $translat->{$name}) { }
662 1 1 unless $self->is_pseudo
679 1 1 if ($dash =~ /^m/)
705 2 1 if ($self->is_pseudo)
711 0 1 if (defined $exe)
712 0 0 unless -e $exe
713 0 0 unless -x $exe
718 0 1 if defined $self->{'_pathstoexe'}
740 0 12 unless $self->is_pseudo
741 0 12 unless defined $cmd
742 0 12 unless grep /^$cmd$/, @{$$self{'_options'}{'_commands'};}
745 0 12 if (defined $exe)
746 0 0 unless -e $exe
747 0 0 unless -x $exe
748 0 0 unless defined $self->{'_pathstoexe'}
753 0 12 if defined $self->{'_pathstoexe'}{$cmd}
777 0 23 if ($self->is_pseudo and not $exe)
778 0 0 if (not $self->command) { }
793 0 23 if ($self->program_dir) { }
797 0 23 if $warn
801 0 46 if -x $path . $_ and not -d $path . $_
23 0 if defined $path
804 23 0 $path ? :
805 0 23 if $warn
806 0 23 if ($path = $self->io->exists_exe($exe)) { }
809 0 0 $self->is_pseudo ? :
0 23 if $warn
869 0 0 unless $self->command
872 0 0 unless grep /^$cmd$/, keys %{$$self{'_options'}{'_composite_commands'};}
900 0 0 unless $self->{'_options'}{'_composite_commands'}
901 0 0 unless $self->{'_options'}{'_composite_commands'}{$cmd}
919 0 0 if defined $self->$opt
942 0 0 if $self->can('command')
945 0 0 unless $cmd
951 0 0 if (defined $filespec and @$filespec)
954 0 0 if @args % 2
968 0 0 if (/^1?>#?(.*)/)
969 0 0 if defined $args{$1}
972 0 0 if (/^2>#?(.*)/)
973 0 0 if defined $args{$1}
976 0 0 if (/^<#?(.*)/)
977 0 0 if defined $args{$1}
980 0 0 if (/^-(.*)\|/) { }
988 0 0 unless $in
989 0 0 unless $out
990 0 0 unless $err
994 0 0 $self->is_pseudo ? :
0 0 unless $exe
1013 0 0 if (ref $files[$_] eq 'ARRAY')
1021 0 0 defined $_ ? :
1023 0 0 defined $_ ? :
1027 0 0 unless IPC::Run::run(\@ipc_args, $in, $out, $err)
1031 0 0 if ($@)
1032 0 0 unless $self->no_throw_on_crash
1053 0 0 if @_
1087 0 0 if ($_ eq '1')
1091 0 0 if (/^s/)
1095 0 0 if (/^d/)
1099 0 0 if (/^m/)
1127 0 0 if @_
1145 0 0 if @_
1164 3 40 if @_
1185 0 0 unless ($tok =~ /^new_/)
1186 0 0 "Can't locate object method '${tok}' via package '" . ref($class) ? :
1214 0 14 unless ($self->can('command') and $self->command or grep /command/, @args)
1220 14 0 if ($cmd)
1222 0 14 unless $self->{'_options'}{'_commands'}
1223 0 14 unless grep /^$cmd$/, @{$$self{'_options'}{'_commands'};}
1288 38 4 unless grep /^[-]?$p$/, @args
1291 40 0 unless grep /^[-]?$s$/, @args
1310 328 11 if @_
1332 3 6 if (not defined $_ or /^a/)
1336 3 3 if (/^p/i)
1340 3 0 if (/^s/i)
1344 0 0 if (/^c/i)
1348 0 0 if (/^f/i)
1379 0 2 if (/^p/i)
1381 0 0 if $self->can($_) and defined $self->$_
1385 0 2 if (/^s/i)
1387 0 0 if $self->can($_) and defined $self->$_
1391 2 0 if (/^a/i)
1393 8 66 if $self->can($_) and defined $self->$_