| line |
true |
false |
branch |
|
42
|
0 |
10 |
if ($self->last_row != 0 or $self->number_columns != 0 or $self->filename) |
|
49
|
0 |
10 |
unless ($filename) |
|
54
|
0 |
10 |
unless $self->open_to_read_fh |
|
61
|
0 |
198 |
unless $line =~ /\w+/ |
|
64
|
0 |
198 |
if (substr($line, 0, 1) eq '#') |
|
78
|
0 |
10 |
unless $self->verify |
|
87
|
0 |
24 |
unless my $filename = $self->check_file($file) |
|
90
|
0 |
24 |
unless $Taste->open_to_read_fh |
|
96
|
12 |
180 |
unless my $line = $Taste->fh->getline |
|
97
|
0 |
180 |
unless $line =~ /\w+/ |
|
98
|
0 |
180 |
if $line =~ /^#/ |
|
105
|
4 |
20 |
if ($Taste->gff) { } |
|
|
12 |
8 |
elsif ($Taste->bed) { } |
|
|
0 |
8 |
elsif ($Taste->ucsc) { } |
|
118
|
0 |
8 |
if ($number == 9) { } |
|
|
0 |
8 |
elsif ($number == 10) { } |
|
|
0 |
8 |
elsif ($number == 11) { } |
|
|
0 |
8 |
elsif ($number == 12) { } |
|
|
0 |
8 |
elsif ($number == 15) { } |
|
|
3 |
5 |
elsif ($number == 16) { } |
|
122
|
0 |
0 |
if $Taste->gff == 2 |
|
128
|
0 |
0 |
if $Taste->ucsc == 10 |
|
131
|
0 |
0 |
if $Taste->ucsc == 10 |
|
137
|
0 |
0 |
if $Taste->ucsc == 11 |
|
140
|
0 |
0 |
if $Taste->ucsc == 11 |
|
146
|
0 |
0 |
if $Taste->ucsc == 12 |
|
149
|
0 |
0 |
if $Taste->bed == 12 |
|
152
|
0 |
0 |
if $Taste->ucsc == 12 |
|
155
|
0 |
0 |
if $Taste->bed == 12 |
|
161
|
0 |
0 |
if $Taste->ucsc == 15 |
|
164
|
0 |
0 |
if $Taste->ucsc == 15 |
|
170
|
0 |
3 |
if $Taste->ucsc == 16 |
|
173
|
3 |
0 |
if $Taste->ucsc == 16 |
|
180
|
0 |
11 |
unless $file =~ /\.g[tf]f\d?(?:\.gz)?$/i |
|
181
|
0 |
11 |
unless my $fh = $self->open_to_read_fh($file) |
|
185
|
11 |
1277 |
unless my $line = $fh->getline |
|
186
|
0 |
1277 |
unless $line =~ /\w+/ |
|
187
|
36 |
1241 |
if $line =~ /^#/ |
|
203
|
60 |
0 |
if (exists $self->{'fh'} and $self->{'fh'}) { } |
|
|
0 |
0 |
elsif ($self->filename) { } |
|
214
|
0 |
60 |
if ($self->last_row != 0 or $self->number_columns != 0) |
|
230
|
0 |
60 |
if ($line2 =~ /[\r\n]+/) |
|
246
|
0 |
137 |
if (not $line =~ /\w+/) { } |
|
|
0 |
137 |
elsif ($line =~ /^# Program (.+)$/) { } |
|
|
10 |
127 |
elsif ($line =~ /^# Database (.+)$/) { } |
|
|
10 |
117 |
elsif ($line =~ /^# Feature (.+)$/) { } |
|
|
0 |
117 |
elsif ($line =~ /^# Column_(\d+)/) { } |
|
|
5 |
112 |
elsif ($line =~ /^##gff-version\s+([\d\.]+)$/) { } |
|
|
0 |
112 |
elsif ($line =~ /^##fileformat=VCFv([\d\.]+)$/) { } |
|
|
44 |
68 |
elsif ($line =~ /^#/) { } |
|
|
8 |
60 |
elsif ($line =~ /^(?:track|browser)\s+/i) { } |
|
311
|
8 |
0 |
if ($line =~ /type=(\w+)/i) |
|
328
|
0 |
60 |
if ($self->_commented_header_line($line)) |
|
341
|
5 |
55 |
if ($format =~ /g[tf]f/i) { } |
|
|
16 |
39 |
elsif ($format =~ /peak/i) { } |
|
|
26 |
13 |
elsif ($format =~ /bg|bdg|bed/i) { } |
|
|
0 |
13 |
elsif ($format =~ /ref+lat|genepred|ucsc/i) { } |
|
|
0 |
13 |
elsif ($format =~ /sgr/i) { } |
|
369
|
13 |
47 |
unless ($self->number_columns) |
|
380
|
77 |
60 |
if ($self->number_columns == 0) { } |
|
390
|
0 |
0 |
if ($self->number_columns == 0 and scalar @{$self->{'comments'};} and $self->{'comments'}[-1] =~ /\t/) |
|
400
|
0 |
0 |
if ($noheader and not $self->bed and not $self->gff and not $self->vcf and not $self->ucsc) |
|
423
|
60 |
0 |
if ($nextline) |
|
425
|
0 |
60 |
if (scalar(@nextdata) - 1 == $self->number_columns) |
|
441
|
60 |
0 |
if $fh |
|
464
|
0 |
574 |
if (index($linedata[-1], "\t") != -1) |
|
478
|
0 |
70 |
unless defined $filename |
|
480
|
0 |
70 |
unless ($extension) |
|
482
|
0 |
0 |
if ($filename =~ /(\.\w+(?:\.gz)?)$/i) |
|
500
|
7 |
1 |
if (scalar @_ == 1) { } |
|
508
|
8 |
0 |
unless (exists $args{'gz'}) |
|
511
|
0 |
8 |
unless ($self->verify) |
|
517
|
0 |
8 |
unless ($args{'filename'} or $self->filename) |
|
527
|
0 |
8 |
if ($extension =~ /(g[tf]f)/i) { } |
|
|
3 |
5 |
elsif ($extension =~ /bedgraph|bed|bdg|narrowpeak|broadpeak/i) { } |
|
|
0 |
5 |
elsif ($extension =~ /vcf/i) { } |
|
|
0 |
5 |
elsif ($extension =~ /sgr/i) { } |
|
|
0 |
5 |
elsif ($extension =~ /reff?lat|genepred|ucsc/i) { } |
|
|
5 |
0 |
elsif ($extension =~ /txt/i) { } |
|
|
0 |
0 |
elsif (not $extension) { } |
|
528
|
0 |
0 |
unless ($self->gff) |
|
530
|
0 |
0 |
$extension =~ /gtf/i ? : |
|
531
|
0 |
0 |
unless ($self->verify and $self->gff) |
|
538
|
1 |
2 |
unless ($self->bed) |
|
541
|
0 |
1 |
unless ($self->verify and $self->bed) |
|
543
|
0 |
0 |
$extension =~ /gz$/i ? : |
|
548
|
0 |
0 |
unless ($self->vcf) |
|
551
|
0 |
0 |
unless ($self->verify and $self->vcf) |
|
553
|
0 |
0 |
$extension =~ /gz$/i ? : |
|
558
|
0 |
0 |
unless ($self->{'extension'} =~ /sgr/i) |
|
564
|
0 |
0 |
if ($self->extension =~ /txt/) |
|
571
|
0 |
0 |
if ($self->ucsc != $self->number_columns) |
|
575
|
0 |
0 |
unless ($self->verify and $self->ucsc) |
|
577
|
0 |
0 |
$extension =~ /gz$/i ? : |
|
590
|
0 |
0 |
if ($self->gff) { } |
|
|
0 |
0 |
elsif ($self->bed) { } |
|
|
0 |
0 |
elsif ($self->ucsc) { } |
|
|
0 |
0 |
elsif ($self->vcf) { } |
|
|
0 |
0 |
elsif ($name =~ /(\.\w{3}(?:\.gz)?)$/i) { } |
|
|
0 |
0 |
elsif ($self->extension) { } |
|
591
|
0 |
0 |
$self->gff == 2.5 ? : |
|
|
0 |
0 |
$self->gff == 3 ? : |
|
594
|
0 |
0 |
if ($self->format) { } |
|
|
0 |
0 |
elsif ($self->number_columns == 4 and $self->name(3) =~ /score/i) { } |
|
609
|
0 |
0 |
if ($self->format) { } |
|
633
|
0 |
0 |
if ($self->extension =~ /g[tf]f/i) { } |
|
|
0 |
0 |
elsif ($self->extension =~ /bed|bdg|peak/i) { } |
|
634
|
0 |
0 |
$self->gff ? : |
|
637
|
0 |
0 |
$self->bed ? : |
|
655
|
8 |
0 |
unless ($args{'format'}) |
|
656
|
0 |
8 |
if (defined $args{'simple'}) { } |
|
|
8 |
0 |
elsif ($extension) { } |
|
662
|
0 |
8 |
if ($extension =~ /sgr|cdt/i) { } |
|
678
|
8 |
0 |
unless (defined $args{'gz'}) |
|
681
|
0 |
8 |
if ($extension =~ /\.vcf\.gz/i) { } |
|
|
0 |
8 |
elsif ($extension =~ /\.gz$/i) { } |
|
694
|
0 |
8 |
if ($args{'gz'} and not $extension =~ /\.gz$/i) { } |
|
|
0 |
8 |
elsif (not $args{'gz'} and $extension =~ /\.gz$/i) { } |
|
704
|
0 |
8 |
if (length $name . $extension > 255) |
|
716
|
0 |
0 |
if (defined $strand_i and $self->gff || $self->bed || $self->ucsc) |
|
718
|
0 |
0 |
if ($self->gff) { } |
|
|
0 |
0 |
elsif ($self->bed or $self->ucsc) { } |
|
721
|
0 |
0 |
if ($s =~ /\d/) |
|
722
|
0 |
0 |
$s == -1 ? : |
|
|
0 |
0 |
$s == 1 ? : |
|
730
|
0 |
0 |
if ($s =~ /\d/) |
|
731
|
0 |
0 |
$s >= 0 ? : |
|
741
|
0 |
8 |
unless defined $fh |
|
745
|
8 |
0 |
if ($args{'format'} eq 'text') |
|
749
|
0 |
8 |
if ($self->gff) |
|
754
|
5 |
0 |
unless ($self->gff or $self->bed or $self->ucsc or $self->vcf or $extension =~ /sgr|kgg|cdt|peak/i) |
|
760
|
0 |
5 |
if ($self->program) |
|
763
|
5 |
0 |
if ($self->database) |
|
766
|
5 |
0 |
if ($self->feature) |
|
775
|
4 |
2 |
unless (/\n$/s) |
|
780
|
5 |
1 |
if (/^#/) { } |
|
800
|
8 |
14 |
if (exists $self->{$i}{'AUTO'} and scalar keys %{$$self{$i};} == $self->{$i}{'AUTO'}) { } |
|
|
14 |
0 |
elsif (scalar keys %{$$self{$i};} == 2) { } |
|
|
0 |
0 |
elsif ($extension =~ /sgr|kgg|cdt/i or $self->ucsc or $self->vcf) { } |
|
826
|
0 |
0 |
if $_ eq 'name' |
|
827
|
0 |
0 |
if $_ eq 'index' |
|
828
|
0 |
0 |
if $_ eq 'AUTO' |
|
842
|
5 |
3 |
if ($self->{'headers'} == 1) |
|
848
|
0 |
8 |
if ($args{'format'} eq 'simple') { } |
|
857
|
0 |
0 |
if ($_ eq '.') { } |
|
894
|
120 |
41 |
ref($self) =~ /^Bio::ToolBox/ ? : |
|
897
|
120 |
41 |
if (not $file and $obj) |
|
900
|
0 |
161 |
unless ($file) |
|
907
|
0 |
161 |
if ($file =~ /\.gz$/i) { } |
|
|
0 |
161 |
elsif ($file =~ /\.bz2$/i) { } |
|
909
|
0 |
0 |
unless $fh = 'IO::File'->new("gzip -dc $file |") |
|
914
|
0 |
0 |
unless $fh = 'IO::File'->new("bzip2 -dc $file |") |
|
919
|
0 |
161 |
unless $fh = 'IO::File'->new($file, 'r') |
|
923
|
120 |
41 |
if ($obj) |
|
935
|
0 |
10 |
unless ($filename) |
|
943
|
0 |
10 |
if (length $name > 255) |
|
949
|
2 |
8 |
unless (defined $gz) |
|
952
|
0 |
2 |
if ($filename =~ /\.vcf(\.gz)?$/i) { } |
|
|
0 |
2 |
elsif ($filename =~ /\.gz$/i) { } |
|
964
|
0 |
10 |
if ($gz == 1 and not $gzip_app) { } |
|
|
0 |
20 |
elsif ($gz == 2 and not $bgzip_app) { } |
|
968
|
0 |
0 |
if ($gzip_app) { } |
|
976
|
0 |
0 |
unless ($gzip_app) |
|
984
|
0 |
0 |
if ($bgzip_app) |
|
989
|
0 |
0 |
unless ($bgzip_app) |
|
993
|
0 |
10 |
$gz == 2 ? : |
|
|
0 |
10 |
$gz == 1 ? : |
|
996
|
8 |
2 |
unless (defined $append) |
|
1004
|
8 |
2 |
if (not $gzipper || $append) { } |
|
|
0 |
2 |
elsif ($gzipper and not $append) { } |
|
|
2 |
0 |
elsif (not $gzipper and $append) { } |
|
|
0 |
0 |
elsif ($gzipper and $append) { } |
|
1005
|
0 |
8 |
unless $fh = 'IO::File'->new($filename, 'w') |
|
1009
|
0 |
0 |
unless $fh = 'IO::File'->new("| $gzipper >$filename") |
|
1013
|
0 |
2 |
unless $fh = 'IO::File'->new(">> $filename") |
|
1017
|
0 |
0 |
unless $fh = 'IO::File'->new("| $gzipper >>$filename") |
|
1020
|
10 |
0 |
if defined $fh |
|
1029
|
60 |
0 |
if (-e $filename) { } |
|
1038
|
0 |
0 |
if (-e $filename . $ext) |
|
1050
|
192 |
0 |
if exists $self->{'fh'} |
|
1056
|
70 |
0 |
if exists $self->{'fh'} and $self->{'fh'} |
|
1066
|
30 |
30 |
if (scalar @{$data->{'comments'};} >= 1) |
|
1073
|
0 |
60 |
if (scalar @commentdata == scalar @linedata) { } |
|
1094
|
0 |
0 |
if ($key eq 'index') |
|
1095
|
0 |
0 |
if ($index != $value) |
|
1107
|
0 |
0 |
unless (exists $temphash{'index'}) |
|
1113
|
0 |
0 |
if (exists $data->{$index}) { } |
|
1139
|
0 |
5 |
if (not $self->gff or $force) |
|
1140
|
0 |
0 |
if (defined $version) { } |
|
|
0 |
0 |
elsif ($self->extension =~ /gtf/i) { } |
|
|
0 |
0 |
elsif ($self->extension =~ /gff3/i) { } |
|
1161
|
45 |
0 |
if ($force or not exists $self->{$i}) |
|
1167
|
45 |
0 |
if ($force or not defined $self->{'column_names'}[$i]) |
|
1174
|
5 |
0 |
if ($force or $self->{'number_columns'} == 0) |
|
1179
|
5 |
0 |
unless $self->{'0'}{'name'} =~ /^#/ |
|
1182
|
5 |
0 |
unless (defined $self->{'feature'}) |
|
1207
|
0 |
27 |
if ($self->format =~ /bedgraph/i or $self->extension =~ /bg|bdg|graph/i) { } |
|
1225
|
200 |
0 |
if ($force or not exists $self->{$i}) |
|
1231
|
200 |
0 |
if ($force or not defined $self->{'column_names'}[$i]) |
|
1238
|
27 |
0 |
unless (defined $self->{'feature'}) |
|
1243
|
27 |
0 |
unless $self->{'0'}{'name'} =~ /^#/ |
|
1258
|
8 |
8 |
if ($self->format =~ /narrow/i or $self->extension =~ /narrow/i) { } |
|
|
0 |
8 |
elsif ($self->format =~ /broad/i or $self->extension =~ /broad/i) { } |
|
|
8 |
0 |
elsif ($self->format =~ /gapped/i or $self->extension =~ /gapped/i) { } |
|
1282
|
200 |
0 |
if ($force or not exists $self->{$i}) |
|
1288
|
200 |
0 |
if ($force or not defined $self->{'column_names'}[$i]) |
|
1295
|
16 |
0 |
unless (defined $self->{'feature'}) |
|
1300
|
16 |
0 |
unless $self->{'0'}{'name'} =~ /^#/ |
|
1321
|
3 |
0 |
if ($column_count == 16) { } |
|
|
0 |
0 |
elsif ($column_count == 15) { } |
|
|
0 |
0 |
elsif ($column_count == 12) { } |
|
|
0 |
0 |
elsif ($column_count == 11) { } |
|
|
0 |
0 |
elsif ($column_count == 10) { } |
|
1346
|
48 |
0 |
if ($force or not exists $self->{$i}) |
|
1352
|
48 |
0 |
if ($force or not defined $self->{'column_names'}[$i]) |
|
1359
|
3 |
0 |
unless (defined $self->{'feature'}) |
|
1364
|
3 |
0 |
unless $self->{'0'}{'name'} =~ /^#/ |
|
1382
|
0 |
0 |
if ($force or not exists $self->{$i}) |
|
1388
|
0 |
0 |
if ($force or not defined $self->{'column_names'}[$i]) |
|
1397
|
0 |
0 |
unless $self->{'0'}{'name'} =~ /^#/ |
|
1400
|
0 |
0 |
unless (defined $self->{'feature'}) |
|
1420
|
0 |
68 |
if (exists $self->{$i}) { } |
|
1421
|
0 |
0 |
unless ($namelist[$i] eq $self->{$i}{'name'}) |
|
1439
|
13 |
0 |
if (scalar @namelist != $self->{'number_columns'}) |
|
1458
|
5 |
46 |
if ($type eq 'gff') { } |
|
|
27 |
19 |
elsif ($type eq 'bed12') { } |
|
|
0 |
19 |
elsif ($type eq 'bed6') { } |
|
|
0 |
19 |
elsif ($type eq 'bdg') { } |
|
|
8 |
11 |
elsif ($type eq 'narrowpeak') { } |
|
|
0 |
11 |
elsif ($type eq 'broadpeak') { } |
|
|
8 |
3 |
elsif ($type eq 'gappedpeak') { } |
|
|
0 |
3 |
elsif ($type eq 'sgr') { } |
|
|
3 |
0 |
elsif ($type eq 'ucsc16') { } |
|
|
0 |
0 |
elsif ($type eq 'ucsc15' or $type eq 'genepredext') { } |
|
|
0 |
0 |
elsif ($type eq 'ucsc12' or $type eq 'knowngene') { } |
|
|
0 |
0 |
elsif ($type eq 'ucsc11' or $type eq 'refflat') { } |
|
|
0 |
0 |
elsif ($type eq 'ucsc10' or $type eq 'genepred') { } |