Condition Coverage

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


and 2 conditions

line l !l condition
413 60 0 $self->number_columns == 0 and scalar @{$self->{'comments'};}

and 3 conditions

line !l l&&!r l&&r condition
226 0 0 60 exists $self->{'fh'} and $self->{'fh'}
413 0 0 0 $self->number_columns == 0 and scalar @{$self->{'comments'};} and $self->{'comments'}[-1] =~ /\t/
423 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
559 0 0 0 $self->verify and $self->gff
569 0 0 1 $self->verify and $self->bed
579 0 0 0 $self->verify and $self->vcf
603 0 0 0 $self->verify and $self->ucsc
622 0 0 0 $self->number_columns == 4 and $self->name(3) =~ /score/i
722 8 0 0 $args{'gz'} and not $extension =~ /\.gz$/i
0 8 0 not $args{'gz'} and $extension =~ /\.gz$/i
744 8 0 0 defined $strand_i and $self->gff || $self->bed || $self->ucsc
828 14 0 8 exists $self->{$i}{'AUTO'} and scalar keys %{$$self{$i};} == $self->{$i}{'AUTO'}
925 41 0 120 not $file and $obj
992 10 0 0 $gz == 1 and not $gzip_app
10 0 0 $gz == 2 and not $bgzip_app
1032 2 0 0 $gzipper and not $append
0 0 2 not $gzipper and $append
0 0 0 $gzipper and $append
1084 0 0 70 exists $self->{'fh'} and $self->{'fh'}

or 2 conditions

line l !l condition
39 0 10 shift() || 0
222 0 60 shift() || 0
534 0 0 $args{'file'} || undef
535 0 8 $args{'format'} ||= undef
921 41 120 shift() || undef
926 120 0 $self->filename || undef
1163 0 5 shift() || undef
1164 0 5 shift() || 0
1237 27 0 shift() || 0
1261 200 0 $bed_names->[$i] || 'extraColumn'
1288 16 0 shift() || 0
1319 200 0 $column_names->[$i] || 'extraColumn'
1349 3 0 shift() || 0
1384 48 0 $column_names->[$i] || 'extraColumn'
1412 0 0 shift() || 0
1420 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
237 0 0 60 $self->last_row != 0 or $self->number_columns != 0
361 8 52 0 $self->format || $self->extension
534 8 0 0 $args{'filename'} ||= $args{'file'} || undef
545 8 0 0 $args{'filename'} or $self->filename
552 8 0 0 $args{'filename'} || $self->filename
744 0 0 0 $self->gff || $self->bed || $self->ucsc
746 0 0 0 $self->bed or $self->ucsc
782 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
828 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
1032 0 2 8 $gzipper || $append
1167 0 0 5 not $self->gff or $force
1195 0 45 0 $force or not exists $self->{$i}
1201 0 45 0 $force or not defined $self->{'column_names'}[$i]
1208 0 5 0 $force or $self->{'number_columns'} == 0
1241 0 0 27 $self->format =~ /bedgraph/i or $self->extension =~ /bg|bdg|graph/i
1260 200 0 0 $force or not exists $self->{$i}
1266 200 0 0 $force or not defined $self->{'column_names'}[$i]
1293 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
1318 200 0 0 $force or not exists $self->{$i}
1324 200 0 0 $force or not defined $self->{'column_names'}[$i]
1383 48 0 0 $force or not exists $self->{$i}
1389 48 0 0 $force or not defined $self->{'column_names'}[$i]
1419 0 0 0 $force or not exists $self->{$i}
1425 0 0 0 $force or not defined $self->{'column_names'}[$i]
1454 65 3 0 $namelist[$i] ||= "Column_$i"
1495 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"