| line |
true |
false |
branch |
|
1017
|
0 |
0 |
unless defined $column |
|
1023
|
0 |
28 |
if @_ |
|
1029
|
0 |
65 |
if @_ |
|
1035
|
0 |
0 |
if @_ |
|
1036
|
0 |
0 |
if (exists $self->{'data'}{'line_count'}) { } |
|
|
0 |
0 |
elsif (exists $self->{'data'}{'header_line_count'}) { } |
|
1049
|
0 |
196 |
if @_ |
|
1052
|
118 |
78 |
wantarray ? : |
|
1057
|
0 |
390 |
unless defined $column |
|
1060
|
83 |
307 |
if (defined $value) |
|
1065
|
389 |
1 |
CORE::length $v ? : |
|
1070
|
1 |
20 |
if ($_[0]) |
|
1073
|
1 |
0 |
if (defined $i) { } |
|
|
0 |
0 |
elsif (exists $self->{'feature'}) { } |
|
1085
|
0 |
20 |
if (exists $self->{'feature'}) |
|
1091
|
20 |
0 |
defined $i ? : |
|
1097
|
5 |
104 |
if ($_[0]) |
|
1100
|
5 |
0 |
$_[0] =~ /^\d+$/ ? : |
|
1101
|
1 |
4 |
if (defined $i and $d) { } |
|
|
0 |
4 |
elsif (not $d) { } |
|
|
4 |
0 |
elsif (exists $self->{'feature'}) { } |
|
1102
|
1 |
0 |
if (substr($self->{'data'}->name($i), -1) eq '0') { } |
|
1122
|
12 |
96 |
if (exists $self->{'feature'}) |
|
1127
|
96 |
0 |
if (defined $i) |
|
1129
|
17 |
79 |
if (substr($self->{'data'}->name($i), -1) eq '0') { } |
|
1143
|
1 |
27 |
if ($_[0]) |
|
1146
|
1 |
0 |
$_[0] =~ /^\d+$/ ? : |
|
1147
|
1 |
0 |
if (defined $i and $d) { } |
|
|
0 |
0 |
elsif (not $d) { } |
|
|
0 |
0 |
elsif (exists $self->{'feature'}) { } |
|
1161
|
0 |
27 |
if (exists $self->{'feature'}) |
|
1168
|
27 |
0 |
defined $i ? : |
|
1175
|
1 |
24 |
if ($_[0]) |
|
1178
|
0 |
1 |
if (defined $i) { } |
|
|
0 |
1 |
elsif (exists $self->{'feature'}) { } |
|
1190
|
4 |
21 |
if (exists $self->{'feature'}) |
|
1196
|
18 |
3 |
defined $i ? : |
|
1202
|
0 |
18 |
if ($str eq '1' or $str eq '-1' or $str eq '0') { } |
|
|
0 |
18 |
elsif ($str eq '+') { } |
|
|
18 |
0 |
elsif ($str eq '-') { } |
|
|
0 |
0 |
elsif ($str eq '.') { } |
|
|
0 |
0 |
elsif ($str eq '2') { } |
|
|
0 |
0 |
elsif ($str eq '*') { } |
|
1230
|
1 |
74 |
if ($_[0]) |
|
1233
|
1 |
0 |
if (defined $i) { } |
|
|
0 |
0 |
elsif (exists $self->{'feature'}) { } |
|
1244
|
4 |
70 |
if (exists $self->{'feature'}) |
|
1249
|
70 |
0 |
if (defined $i) { } |
|
|
0 |
0 |
elsif (my $att = $self->gff_attributes) { } |
|
1260
|
0 |
3 |
if @_ |
|
1266
|
0 |
0 |
exists $self->{'feature'} ? : |
|
|
3 |
0 |
defined $start_i ? : |
|
1268
|
3 |
0 |
if $end |
|
1269
|
3 |
0 |
CORE::length $coord > 2 ? : |
|
1274
|
1 |
8 |
if ($_[0]) |
|
1277
|
0 |
1 |
if (defined $i) { } |
|
|
0 |
1 |
elsif (exists $self->{'feature'}) { } |
|
1289
|
0 |
9 |
if (defined $i) |
|
1293
|
4 |
5 |
if (exists $self->{'feature'}) |
|
1297
|
5 |
0 |
if ($self->{'data'}->feature) |
|
1306
|
0 |
65 |
if @_ |
|
1308
|
65 |
0 |
if defined $i |
|
1309
|
65 |
0 |
if (defined $v and $v ne '.') |
|
1312
|
0 |
0 |
if exists $self->{'feature'} |
|
1313
|
0 |
0 |
if (my $att = $self->gff_attributes) |
|
1321
|
0 |
0 |
if @_ |
|
1322
|
0 |
0 |
if ($self->{'data'}->vcf) |
|
1328
|
0 |
0 |
if (defined $s and defined $e) { } |
|
|
0 |
0 |
elsif (defined $s) { } |
|
1342
|
0 |
0 |
defined $c ? : |
|
1347
|
0 |
0 |
if $self->{'data'}->gff |
|
1348
|
0 |
0 |
if $self->{'data'}->vcf |
|
1354
|
0 |
0 |
unless $self->{'data'}->gff |
|
1355
|
0 |
0 |
if exists $self->{'attributes'} |
|
1359
|
0 |
0 |
unless $tag and $value |
|
1370
|
0 |
0 |
unless $self->{'data'}->vcf |
|
1371
|
0 |
0 |
if exists $self->{'attributes'} |
|
1376
|
0 |
0 |
if ($self->{'data'}->name(7) eq 'INFO') |
|
1377
|
0 |
0 |
defined $_->[1] ? : |
|
1386
|
0 |
0 |
if ($self->{'data'}->number_columns > 8) |
|
1392
|
0 |
0 |
defined $sampleVals[$_] ? : |
|
1403
|
0 |
0 |
if $self->{'data'}->gff |
|
1404
|
0 |
0 |
if $self->{'data'}->vcf |
|
1410
|
0 |
0 |
unless $self->{'data'}->gff |
|
1411
|
0 |
0 |
unless exists $self->{'attributes'} |
|
1413
|
0 |
0 |
if (exists $self->{'attributes'}{'ID'}) |
|
1417
|
0 |
0 |
if (exists $self->{'attributes'}{'Name'}) |
|
1423
|
0 |
0 |
if $key eq 'ID' |
|
1424
|
0 |
0 |
if $key eq 'Name' |
|
1436
|
0 |
0 |
unless $self->{'data'}->vcf |
|
1437
|
0 |
0 |
unless exists $self->{'attributes'} |
|
1443
|
0 |
0 |
defined $self->{'attributes'}{'INFO'}{$_} ? : |
|
1453
|
0 |
0 |
if exists $self->{'attributes'}{'9'}{'GT'} |
|
1455
|
0 |
0 |
if $key eq 'GT' |
|
1458
|
0 |
0 |
if (@order) { } |
|
1467
|
0 |
0 |
if (@order) { } |
|
1485
|
0 |
9 |
if @_ |
|
1486
|
0 |
9 |
if exists $self->{'feature'} |
|
1489
|
9 |
0 |
unless $self->feature_type eq 'named' or $force |
|
1493
|
0 |
0 |
if ($f) |
|
1499
|
0 |
0 |
unless $self->{'data'}->database |
|
1506
|
0 |
0 |
unless $f |
|
1513
|
0 |
1 |
if @_ |
|
1514
|
0 |
1 |
unless $self->{'data'}->database |
|
1515
|
1 |
0 |
if ($self->feature_type eq 'coordinate') { } |
|
|
0 |
0 |
elsif ($self->feature_type eq 'named') { } |
|
1520
|
1 |
0 |
$db ? : |
|
1524
|
0 |
0 |
$f ? : |
|
1535
|
0 |
0 |
unless defined $db |
|
1536
|
0 |
0 |
unless $db->can('features') |
|
1556
|
0 |
0 |
if ($self->feature_type eq 'named' and $args{'subfeature'}) |
|
1566
|
0 |
0 |
if (exists $args{'strand'}) |
|
1568
|
0 |
0 |
$args{'strand'} =~ /\-|r/i ? : |
|
1570
|
0 |
0 |
if (exists $args{'extend'} and $args{'extend'}) |
|
1572
|
0 |
0 |
if $start <= 0 |
|
1575
|
0 |
0 |
unless defined $seqid and defined $start and defined $stop |
|
1579
|
0 |
0 |
if ($strand == -1) |
|
1591
|
0 |
0 |
unless (@$subfeatures) |
|
1602
|
0 |
0 |
unless $Bio::ToolBox::Data::Feature::a->[1] <=> $Bio::ToolBox::Data::Feature::b->[1] |
|
1614
|
0 |
0 |
if ($self->strand == -1) |
|
1626
|
0 |
0 |
unless ($GENETOOL_LOADED) |
|
1629
|
0 |
0 |
if ($@) { } |
|
1639
|
0 |
0 |
unless $feature |
|
1643
|
0 |
0 |
if ($subf eq 'exon') { } |
|
|
0 |
0 |
elsif ($subf eq 'cds') { } |
|
|
0 |
0 |
elsif ($subf eq '5p_utr') { } |
|
|
0 |
0 |
elsif ($subf eq '3p_utr') { } |
|
|
0 |
0 |
elsif ($subf eq 'intron') { } |
|
1672
|
0 |
7 |
unless ($args{'dataset'}) |
|
1678
|
0 |
0 |
if ($self->feature_type eq 'named' and $args{'subfeature'}) |
|
1687
|
7 |
0 |
if ($self->feature_type eq 'coordinate') { } |
|
|
0 |
0 |
elsif ($self->feature_type eq 'named') { } |
|
1693
|
0 |
7 |
exists $args{'strand'} && defined $args{'strand'} ? : |
|
1698
|
0 |
0 |
unless $f |
|
1703
|
0 |
0 |
exists $args{'strand'} && defined $args{'strand'} ? : |
|
1710
|
0 |
0 |
if (exists $args{'extend'} and $args{'extend'}) |
|
1716
|
0 |
7 |
if $params[1] <= 0 |
|
1717
|
0 |
7 |
if ($params[2] < $params[1]) |
|
1719
|
0 |
0 |
if $params[2] <= 0 |
|
1725
|
0 |
7 |
unless $params[0] and defined $params[1] |
|
1745
|
0 |
0 |
unless (@$subfeatures) |
|
1749
|
0 |
0 |
if exists $args->{'exon'} |
|
1760
|
0 |
0 |
defined $args->{'strand'} ? : |
|
1768
|
0 |
0 |
if defined $exon_scores |
|
1782
|
0 |
1 |
unless ($args{'dataset'}) |
|
1792
|
0 |
1 |
unless ($args{'extend'}) |
|
1795
|
0 |
1 |
unless $args{'db'} or $self->{'data'}->open_meta_database |
|
1798
|
1 |
0 |
unless defined $args{'coordinate'} |
|
1804
|
0 |
1 |
if $params[1] < 1 |
|
1806
|
0 |
1 |
defined $args{'strand'} ? : |
|
1817
|
0 |
1 |
if ($args{'avoid'}) |
|
1822
|
0 |
1 |
if ($args{'absolute'}) { } |
|
1824
|
0 |
0 |
wantarray ? : |
|
1840
|
0 |
4 |
unless ($args{'dataset'}) |
|
1849
|
0 |
4 |
unless $args{'db'} or $self->{'data'}->open_meta_database |
|
1853
|
0 |
0 |
if ($self->feature_type eq 'named' and $args{'subfeature'}) |
|
1865
|
0 |
4 |
defined $args{'strand'} ? : |
|
1866
|
0 |
4 |
if ($args{'extend'}) |
|
1869
|
0 |
0 |
if $params[1] < 1 |
|
1881
|
0 |
4 |
if ($args{'avoid'}) |
|
1886
|
0 |
4 |
if ($args{'absolute'}) { } |
|
1888
|
0 |
0 |
wantarray ? : |
|
1892
|
4 |
0 |
unless defined $args{'coordinate'} |
|
1903
|
0 |
0 |
unless (@$subfeatures) |
|
1907
|
0 |
0 |
if exists $args->{'exon'} |
|
1925
|
0 |
0 |
defined $args->{'strand'} ? : |
|
1952
|
0 |
0 |
if ($args->{'extend'}) |
|
1984
|
0 |
0 |
if ($args->{'absolute'}) { } |
|
1986
|
0 |
0 |
wantarray ? : |
|
2002
|
0 |
5 |
defined $args->{'strand'} ? : |
|
2003
|
0 |
5 |
if ($args->{'position'} == 5 and $strand >= 0) { } |
|
|
0 |
5 |
elsif ($args->{'position'} == 3 and $strand >= 0) { } |
|
|
5 |
0 |
elsif ($args->{'position'} == 5 and $strand < 0) { } |
|
|
0 |
0 |
elsif ($args->{'position'} == 3 and $strand < 0) { } |
|
|
0 |
0 |
elsif ($args->{'position'} == 4) { } |
|
2029
|
0 |
0 |
if (ref $args->{'avoid'} eq 'ARRAY') { } |
|
|
0 |
0 |
elsif ($args->{'avoid'} eq '1') { } |
|
|
0 |
0 |
elsif ($args->{'avoid'} =~ /w+/i) { } |
|
2034
|
0 |
0 |
if (defined $args->{'type'}) { } |
|
2058
|
0 |
0 |
if (@overlap_features) |
|
2067
|
0 |
0 |
if $feat->primary_id eq $primary |
|
2074
|
0 |
0 |
if ($position >= $start and $position <= $stop) |
|
2089
|
0 |
5 |
if ($strand >= 0) { } |
|
|
5 |
0 |
elsif ($strand < 0) { } |
|
2099
|
5 |
0 |
wantarray ? : |
|
2107
|
0 |
0 |
if ($method eq 'ncount') { } |
|
2110
|
0 |
0 |
unless $p >= $start and $p <= $end |
|
2112
|
0 |
0 |
if (exists $namecheck->{$n}) { } |
|
2128
|
0 |
0 |
unless $p >= $start and $p <= $end |
|
2143
|
0 |
0 |
unless ($args{'db'}) |
|
2146
|
0 |
0 |
unless ($args{'data'} and ref $args{'data'} eq 'HASH') |
|
2149
|
0 |
0 |
unless ($args{'callback'}) |
|
2155
|
0 |
0 |
if ($self->feature_type eq 'named' and $args{'subfeature'}) { } |
|
2160
|
0 |
0 |
if (@$subfeatures) { } |
|
2187
|
0 |
0 |
unless defined $tid |
|
2216
|
0 |
0 |
unless $args{'bed'} =~ /^\d+$/ |
|
2217
|
0 |
0 |
unless $args{'bed'} >= 3 |
|
2225
|
0 |
0 |
if ($chr eq '.' or not CORE::length $chr or $start eq '.' or not CORE::length $start) |
|
2233
|
0 |
0 |
if ($args{'bed'} >= 4) |
|
2237
|
0 |
0 |
if ($args{'bed'} >= 5) |
|
2238
|
0 |
0 |
exists $args{'score'} ? : |
|
2239
|
0 |
0 |
unless defined $score |
|
2242
|
0 |
0 |
if ($args{'bed'} >= 6) |
|
2244
|
0 |
0 |
if (exists $args{'strand'} and defined $args{'strand'}) { } |
|
2250
|
0 |
0 |
$s == -1 ? : |
|
2269
|
0 |
0 |
if ($chr eq '.' or not CORE::length $chr or $start eq '.' or not CORE::length $start) |
|
2274
|
0 |
0 |
if (exists $args{'strand'} and defined $args{'strand'}) { } |
|
2280
|
0 |
0 |
$strand == 1 ? : |
|
|
0 |
0 |
$strand == -1 ? : |
|
2285
|
0 |
0 |
if (defined $type and $type =~ /:/) |
|
2288
|
0 |
0 |
unless ($source) |
|
2291
|
0 |
0 |
unless ($primary_tag) |
|
2292
|
0 |
0 |
$args{'primary_tag'} || defined $type ? : |
|
2296
|
0 |
0 |
exists $args{'score'} ? : |
|
2297
|
0 |
0 |
unless defined $score |
|
2305
|
0 |
0 |
if (exists $args{'attributes'} and ref $args{'attributes'} eq 'ARRAY') |