Condition Coverage

blib/lib/Bio/ToolBox/Data/file.pm
Criterion Covered Total %
condition 65 211 30.8


and 2 conditions

line l !l condition
390 60 0 $self->number_columns == 0 and scalar @{$self->{'comments'};}

and 3 conditions

line !l l&&!r l&&r condition
203 0 0 60 exists $self->{'fh'} and $self->{'fh'}
390 0 0 0 $self->number_columns == 0 and scalar @{$self->{'comments'};} and $self->{'comments'}[-1] =~ /\t/
400 60 0 0 $noheader and not $self->bed
60 0 0 $noheader and not $self->bed and not $self->gff
0 0 0 $noheader and not $self->bed and not $self->gff and not $self->vcf
0 0 0 $noheader and not $self->bed and not $self->gff and not $self->vcf and not $self->ucsc
531 0 0 0 $self->verify and $self->gff
541 0 0 1 $self->verify and $self->bed
551 0 0 0 $self->verify and $self->vcf
575 0 0 0 $self->verify and $self->ucsc
594 0 0 0 $self->number_columns == 4 and $self->name(3) =~ /score/i
694 8 0 0 $args{'gz'} and not $extension =~ /\.gz$/i
0 8 0 not $args{'gz'} and $extension =~ /\.gz$/i
716 8 0 0 defined $strand_i and $self->gff || $self->bed || $self->ucsc
800 14 0 8 exists $self->{$i}{'AUTO'} and scalar keys %{$$self{$i};} == $self->{$i}{'AUTO'}
897 41 0 120 not $file and $obj
964 10 0 0 $gz == 1 and not $gzip_app
10 0 0 $gz == 2 and not $bgzip_app
1004 2 0 0 $gzipper and not $append
0 0 2 not $gzipper and $append
0 0 0 $gzipper and $append
1056 0 0 70 exists $self->{'fh'} and $self->{'fh'}

or 2 conditions

line l !l condition
39 0 10 shift() || 0
199 0 60 shift() || 0
506 0 0 $args{'file'} || undef
507 0 8 $args{'format'} ||= undef
893 41 120 shift() || undef
898 120 0 $self->filename || undef
1135 0 5 shift() || undef
1136 0 5 shift() || 0
1203 27 0 shift() || 0
1226 200 0 $bed_names->[$i] || 'extraColumn'
1253 16 0 shift() || 0
1283 200 0 $column_names->[$i] || 'extraColumn'
1313 3 0 shift() || 0
1347 48 0 $column_names->[$i] || 'extraColumn'
1375 0 0 shift() || 0
1383 0 0 $column_names->[$i] || 'extraColumn'

or 3 conditions

line l !l&&r !l&&!r condition
42 0 0 10 $self->last_row != 0 or $self->number_columns != 0
0 0 10 $self->last_row != 0 or $self->number_columns != 0 or $self->filename
214 0 0 60 $self->last_row != 0 or $self->number_columns != 0
338 13 47 0 $self->format || $self->extension
506 8 0 0 $args{'filename'} ||= $args{'file'} || undef
517 8 0 0 $args{'filename'} or $self->filename
524 8 0 0 $args{'filename'} || $self->filename
716 0 0 0 $self->gff || $self->bed || $self->ucsc
718 0 0 0 $self->bed or $self->ucsc
754 0 3 5 $self->gff or $self->bed
3 0 5 $self->gff or $self->bed or $self->ucsc
3 0 5 $self->gff or $self->bed or $self->ucsc or $self->vcf
0 0 5 $self->gff or $self->bed or $self->ucsc or $self->vcf or $extension =~ /sgr|kgg|cdt|peak/i
800 0 0 0 $extension =~ /sgr|kgg|cdt/i or $self->ucsc
0 0 0 $extension =~ /sgr|kgg|cdt/i or $self->ucsc or $self->vcf
1004 0 2 8 $gzipper || $append
1139 0 0 5 not $self->gff or $force
1161 0 45 0 $force or not exists $self->{$i}
1167 0 45 0 $force or not defined $self->{'column_names'}[$i]
1174 0 5 0 $force or $self->{'number_columns'} == 0
1207 0 0 27 $self->format =~ /bedgraph/i or $self->extension =~ /bg|bdg|graph/i
1225 200 0 0 $force or not exists $self->{$i}
1231 200 0 0 $force or not defined $self->{'column_names'}[$i]
1258 0 8 8 $self->format =~ /narrow/i or $self->extension =~ /narrow/i
0 0 8 $self->format =~ /broad/i or $self->extension =~ /broad/i
8 0 0 $self->format =~ /gapped/i or $self->extension =~ /gapped/i
1282 200 0 0 $force or not exists $self->{$i}
1288 200 0 0 $force or not defined $self->{'column_names'}[$i]
1346 48 0 0 $force or not exists $self->{$i}
1352 48 0 0 $force or not defined $self->{'column_names'}[$i]
1382 0 0 0 $force or not exists $self->{$i}
1388 0 0 0 $force or not defined $self->{'column_names'}[$i]
1417 65 3 0 $namelist[$i] ||= "Column_$i"
1458 0 0 0 $type eq 'ucsc15' or $type eq 'genepredext'
0 0 0 $type eq 'ucsc12' or $type eq 'knowngene'
0 0 0 $type eq 'ucsc11' or $type eq 'refflat'
0 0 0 $type eq 'ucsc10' or $type eq 'genepred'