| line |
true |
false |
branch |
|
35
|
26 |
46 |
if (ref $class) |
|
77
|
0 |
52 |
unless (defined $self->{'data_table'} and ref $self->{'data_table'} eq 'ARRAY') |
|
81
|
0 |
0 |
unless $silence |
|
87
|
52 |
0 |
if (defined $self->{'last_row'}) { } |
|
89
|
0 |
52 |
if ($self->{'last_row'} != $number) |
|
103
|
52 |
0 |
if (defined $self->{'number_columns'}) { } |
|
110
|
0 |
945 |
if ($count != $number) |
|
112
|
0 |
0 |
if $count < $number |
|
113
|
0 |
0 |
if $count > $number |
|
123
|
0 |
52 |
if (@problems) |
|
129
|
0 |
0 |
if ($too_low) |
|
130
|
0 |
0 |
unless $silence |
|
134
|
0 |
0 |
if ($too_high) |
|
135
|
0 |
0 |
unless $silence |
|
151
|
0 |
415 |
unless ($self->{$i}{'name'} eq $self->{'data_table'}[0][$i]) |
|
158
|
0 |
0 |
unless $silence |
|
161
|
0 |
415 |
unless ($self->{$i}{'index'} == $i) |
|
163
|
0 |
0 |
unless $silence |
|
167
|
0 |
52 |
if $mdcheck |
|
173
|
6 |
46 |
if ($self->{'gff'}) |
|
179
|
1 |
5 |
if ($self->{'number_columns'} != 9) |
|
185
|
0 |
6 |
if (exists $self->{'0'} and not $self->{'0'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
194
|
0 |
6 |
if (exists $self->{'3'} and not $self->{'3'}{'name'} =~ /start|pos|position/i) |
|
202
|
0 |
6 |
if (exists $self->{'4'} and not $self->{'4'}{'name'} =~ /stop|end|pos|position/i) |
|
210
|
0 |
6 |
if (exists $self->{'6'} and not $self->{'6'}{'name'} =~ /strand/i) |
|
220
|
0 |
6 |
unless ($self->_column_is_integers(3, 4)) |
|
224
|
0 |
6 |
unless ($self->_column_is_numeric(5)) |
|
228
|
0 |
6 |
unless ($self->_column_is_stranded(6)) |
|
234
|
1 |
5 |
if ($gff_check == 0) |
|
241
|
8 |
0 |
if (exists $self->{$i}{'AUTO'}) |
|
245
|
0 |
1 |
unless $silence |
|
250
|
21 |
31 |
if ($self->{'bed'}) |
|
256
|
0 |
21 |
if ($self->{'number_columns'} < 3) |
|
262
|
0 |
21 |
if (exists $self->{'0'} and not $self->{'0'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
270
|
0 |
21 |
if (exists $self->{'1'} and not $self->{'1'}{'name'} =~ /start|pos|position/i) |
|
277
|
0 |
21 |
if (exists $self->{'2'} and not $self->{'2'}{'name'} =~ /stop|end|pos|position/i) |
|
284
|
0 |
21 |
if (exists $self->{'5'} and not $self->{'5'}{'name'} =~ /strand/i) |
|
291
|
0 |
11 |
if (exists $self->{'6'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'6'}{'name'} =~ /start|thick|cds/i) |
|
299
|
0 |
11 |
if (exists $self->{'7'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'7'}{'name'} =~ /end|stop|thick|cds/i) |
|
307
|
0 |
11 |
if (exists $self->{'8'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'8'}{'name'} =~ /item|rgb|color/i) |
|
315
|
0 |
11 |
if (exists $self->{'9'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'9'}{'name'} =~ /count|number|block|exon/i) |
|
323
|
0 |
21 |
if (exists $self->{'10'} and not $self->{'10'}{'name'} =~ /size|length|block|exon/i) |
|
330
|
0 |
21 |
if (exists $self->{'11'} and not $self->{'11'}{'name'} =~ /start|block|exon/i) |
|
339
|
0 |
21 |
unless ($self->_column_is_integers(1, 2)) |
|
343
|
15 |
6 |
if ($self->{'number_columns'} >= 5) |
|
345
|
0 |
15 |
unless ($self->_column_is_numeric(4)) |
|
350
|
15 |
6 |
if ($self->{'number_columns'} >= 6) |
|
352
|
0 |
15 |
unless ($self->_column_is_stranded(5)) |
|
357
|
4 |
17 |
if ($self->{'format'} and $self->{'format'} =~ /narrow|broad/i) |
|
359
|
0 |
4 |
unless ($self->_column_is_numeric(6, 7, 8)) |
|
364
|
3 |
18 |
if ($self->{'number_columns'} == 12) |
|
366
|
0 |
3 |
unless ($self->_column_is_integers(6, 7, 9)) |
|
370
|
0 |
3 |
unless ($self->_column_is_comma_integers(10, 11)) |
|
375
|
4 |
17 |
if ($self->{'number_columns'} == 15 and $self->{'format'} =~ /gapped/i) |
|
380
|
0 |
4 |
unless ($self->_column_is_integers(6, 7, 9)) |
|
384
|
0 |
4 |
unless ($self->_column_is_comma_integers(10, 11)) |
|
388
|
0 |
4 |
unless ($self->_column_is_numeric(12, 13, 14)) |
|
395
|
0 |
18 |
if ($self->{'format'} and $self->{'format'} =~ /narrowpeak/i and $self->{'number_columns'} != 10) |
|
402
|
0 |
18 |
if ($self->{'format'} and $self->{'format'} =~ /broadpeak/i and $self->{'number_columns'} != 9) |
|
409
|
0 |
18 |
if ($self->{'format'} and $self->{'format'} =~ /gappedpeak/i and $self->{'number_columns'} != 15) |
|
418
|
21 |
0 |
if ($bed_check) { } |
|
432
|
0 |
0 |
if (exists $self->{$i}{'AUTO'}) |
|
436
|
0 |
0 |
unless $silence |
|
441
|
6 |
46 |
if ($self->{'ucsc'}) |
|
448
|
6 |
0 |
if ($colnumber == 16) { } |
|
|
0 |
0 |
elsif ($colnumber == 15 or $colnumber == 12) { } |
|
|
0 |
0 |
elsif ($colnumber == 11) { } |
|
|
0 |
0 |
elsif ($colnumber == 10) { } |
|
454
|
0 |
6 |
unless ($self->{'2'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
459
|
3 |
3 |
unless ($self->{'4'}{'name'} =~ /start|position/i) |
|
463
|
3 |
3 |
unless ($self->{'5'}{'name'} =~ /stop|end|position/i) |
|
467
|
3 |
3 |
unless ($self->{'6'}{'name'} =~ /start|position/i) |
|
471
|
3 |
3 |
unless ($self->{'7'}{'name'} =~ /stop|end|position/i) |
|
475
|
0 |
6 |
unless ($self->_column_is_integers(4, 5, 6, 7, 8)) |
|
479
|
0 |
6 |
unless ($self->_column_is_comma_integers(9, 10)) |
|
483
|
0 |
6 |
unless ($self->_column_is_stranded(3)) |
|
489
|
0 |
0 |
$colnumber == 15 ? : |
|
497
|
0 |
0 |
unless ($self->{'1'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
502
|
0 |
0 |
unless ($self->{'3'}{'name'} =~ /start|position/i) |
|
506
|
0 |
0 |
unless ($self->{'4'}{'name'} =~ /stop|end|position/i) |
|
510
|
0 |
0 |
unless ($self->{'5'}{'name'} =~ /start|position/i) |
|
514
|
0 |
0 |
unless ($self->{'6'}{'name'} =~ /stop|end|position/i) |
|
518
|
0 |
0 |
unless ($self->_column_is_integers(3, 4, 5, 6, 7)) |
|
522
|
0 |
0 |
unless ($self->_column_is_comma_integers(8, 9)) |
|
526
|
0 |
0 |
unless ($self->_column_is_stranded(2)) |
|
535
|
0 |
0 |
unless ($self->{'2'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
540
|
0 |
0 |
unless ($self->{'4'}{'name'} =~ /start|position/i) |
|
544
|
0 |
0 |
unless ($self->{'5'}{'name'} =~ /stop|end|position/i) |
|
548
|
0 |
0 |
unless ($self->{'6'}{'name'} =~ /start|position/i) |
|
552
|
0 |
0 |
unless ($self->{'7'}{'name'} =~ /stop|end|position/i) |
|
556
|
0 |
0 |
unless ($self->_column_is_integers(4, 5, 6, 7, 8)) |
|
560
|
0 |
0 |
unless ($self->_column_is_comma_integers(9, 10)) |
|
564
|
0 |
0 |
unless ($self->_column_is_stranded(3)) |
|
573
|
0 |
0 |
unless ($self->{'1'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
578
|
0 |
0 |
unless ($self->{'3'}{'name'} =~ /start|position/i) |
|
582
|
0 |
0 |
unless ($self->{'4'}{'name'} =~ /stop|end|position/i) |
|
586
|
0 |
0 |
unless ($self->{'5'}{'name'} =~ /start|position/i) |
|
590
|
0 |
0 |
unless ($self->{'6'}{'name'} =~ /stop|end|position/i) |
|
594
|
0 |
0 |
unless ($self->_column_is_integers(3, 4, 5, 6, 7)) |
|
598
|
0 |
0 |
unless ($self->_column_is_comma_integers(8, 9)) |
|
602
|
0 |
0 |
unless ($self->_column_is_stranded(2)) |
|
613
|
3 |
3 |
if ($ucsc_check == 0) |
|
623
|
48 |
0 |
if (exists $self->{$i}{'AUTO'}) |
|
627
|
0 |
3 |
unless $silence |
|
632
|
0 |
52 |
if ($self->{'vcf'}) |
|
638
|
0 |
0 |
if ($self->{'number_columns'} < 8) |
|
644
|
0 |
0 |
unless ($self->{'0'}{'name'} =~ /chrom/i) |
|
648
|
0 |
0 |
if (exists $self->{'1'} and not $self->{'1'}{'name'} =~ /^pos|start/i) |
|
657
|
0 |
0 |
unless ($self->_column_is_integers(1)) |
|
663
|
0 |
0 |
if ($vcf_check) { } |
|
665
|
0 |
0 |
if $self->{'vcf'} == 1 |
|
675
|
0 |
0 |
if (exists $self->{$i}{'AUTO'}) |
|
679
|
0 |
0 |
unless $silence |
|
684
|
0 |
52 |
if (exists $self->{'extension'} and defined $self->{'extension'} and $self->{'extension'} =~ /sgr/i) |
|
692
|
0 |
0 |
if ($self->{'number_columns'} != 3) |
|
696
|
0 |
0 |
unless ($self->{'0'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
700
|
0 |
0 |
unless ($self->{'1'}{'name'} =~ /start|position/i) |
|
704
|
0 |
0 |
unless ($self->_column_is_integers(1)) |
|
708
|
0 |
0 |
if ($sgr_check == 0) |
|
719
|
0 |
0 |
if (exists $self->{$i}{'AUTO'}) |
|
723
|
0 |
0 |
unless $silence |
|
729
|
29 |
23 |
if ($self->{'bed'} or $self->{'gff'} or $self->{'ucsc'} or $self->{'extension'} and $self->{'extension'} =~ /sgr/i) { } |
|
|
18 |
10 |
elsif ($self->{'bed'} == 0 and $self->{'gff'} == 0 and $self->{'ucsc'} == 0 and ($self->{'extension'} and not $self->{'extension'} =~ /sgr/i)) { } |
|
743
|
18 |
0 |
unless $self->{'headers'} == -1 |
|
755
|
2 |
38 |
if $self->{'last_row'} == 0 |
|
757
|
0 |
101 |
unless exists $self->{$_} |
|
761
|
0 |
1648 |
unless $self->{'data_table'}[$row][$i] =~ /^\d+$/ |
|
771
|
0 |
29 |
if $self->{'last_row'} == 0 |
|
773
|
0 |
45 |
unless exists $self->{$_} |
|
778
|
0 |
407 |
unless $self->{'data_table'}[$row][$i] =~ /^[\d\-\+\.,eE]+$/ |
|
790
|
0 |
13 |
if $self->{'last_row'} == 0 |
|
792
|
0 |
26 |
unless exists $self->{$_} |
|
796
|
0 |
220 |
unless $self->{'data_table'}[$row][$i] =~ /^[\d,]+$/ |
|
805
|
0 |
27 |
unless exists $self->{$index} |
|
807
|
0 |
347 |
unless $self->{'data_table'}[$row][$index] =~ /^(?:\-1|0|1|\+|\-|\.)$/ |
|
820
|
1 |
0 |
if (not defined $_[0]) { } |
|
|
0 |
0 |
elsif ($_[0] eq '0' or $_[0] eq '1') { } |
|
|
0 |
0 |
elsif ($_[0] =~ /[a-zA-Z]+/) { } |
|
840
|
0 |
15 |
unless $self->{'db'} |
|
841
|
0 |
15 |
if $self->{'db'} =~ /^Parsed:/ |
|
842
|
14 |
1 |
if (exists $self->{'db_connection'}) |
|
843
|
14 |
0 |
unless $force |
|
846
|
0 |
1 |
unless $db |
|
860
|
0 |
12 |
unless $dataset |
|
861
|
11 |
1 |
if (exists $self->{'verfied_dataset'}{$dataset}) { } |
|
865
|
0 |
1 |
if ($dataset =~ /^(?:file|http|ftp)/) |
|
876
|
1 |
0 |
if ($verified) |
|
892
|
0 |
2 |
if (ref $self eq 'Bio::ToolBox::Data::Stream') |
|
893
|
0 |
0 |
unless ($self->mode) |
|
897
|
0 |
0 |
if (defined $self->{'fh'}) |
|
903
|
0 |
2 |
unless (@_) |
|
913
|
2 |
16 |
if ($i == $deletion_list[0]) { } |
|
929
|
0 |
3 |
if (ref $self eq 'Bio::ToolBox::Data::Stream') |
|
930
|
0 |
0 |
unless ($self->mode) |
|
934
|
0 |
0 |
if (defined $self->{'fh'}) |
|
942
|
0 |
3 |
unless (@_) |
|
973
|
2 |
1 |
if exists $self->{'column_indices'} |
|
974
|
0 |
2 |
if ($self->gff or $self->bed or $self->ucsc or $self->vcf) |
|
987
|
19 |
33 |
if (@_) |
|
995
|
0 |
40 |
if @_ |
|
996
|
28 |
12 |
if (defined $self->{'feature_type'}) |
|
1000
|
7 |
5 |
if (defined $self->chromo_column and defined $self->start_column) { } |
|
|
5 |
0 |
elsif (defined $self->id_column or defined $self->type_column and defined $self->name_column or defined $self->feature and defined $self->name_column) { } |
|
1018
|
60 |
8 |
if (@_) |
|
1026
|
19 |
26 |
if (@_) |
|
1028
|
0 |
0 |
if (exists $self->{'db_connection'} and $self->{'db_connection'}) |
|
1047
|
59 |
123 |
if (defined $_[0]) |
|
1055
|
5 |
86 |
if (defined $_[0] and $_[0] =~ /^(?:0|1|2|2\.[2|5]|3)$/) |
|
1057
|
0 |
5 |
if ($_[0] eq '2.2' or $_[0] eq '2.5') { } |
|
|
5 |
0 |
elsif ($_[0] eq '3') { } |
|
1073
|
43 |
91 |
if (defined $_[0] and $_[0] =~ /^\d+$/) |
|
1081
|
3 |
53 |
if (defined $_[0] and $_[0] =~ /^\d+$/) |
|
1089
|
0 |
39 |
if (defined $_[0] and $_[0] =~ /^[\d\.]+$/) |
|
1097
|
0 |
552 |
if @_ |
|
1103
|
0 |
0 |
if @_ |
|
1110
|
0 |
892 |
if @_ |
|
1116
|
0 |
138 |
if @_ |
|
1122
|
0 |
29 |
if @_ |
|
1128
|
0 |
0 |
if @_ |
|
1134
|
0 |
124 |
if @_ |
|
1153
|
0 |
53 |
unless my $comment = shift() |
|
1162
|
1 |
0 |
if (defined $index) { } |
|
1172
|
0 |
0 |
unless $self->vcf |
|
1173
|
0 |
0 |
if exists $self->{'vcf_headers'} |
|
1177
|
0 |
0 |
if ($comment =~ /^##([\w\-\.]+)=(.+)$/) { } |
|
1185
|
0 |
0 |
if (not $value =~ /^<.+>$/) { } |
|
1204
|
0 |
0 |
unless $self->vcf |
|
1205
|
0 |
0 |
unless exists $self->{'vcf_headers'} |
|
1214
|
0 |
0 |
if $key eq 'fileformat' |
|
1215
|
0 |
0 |
if (ref $self->{'vcf_headers'}{$key} eq 'HASH') { } |
|
1243
|
0 |
4 |
if @_ |
|
1248
|
2 |
2 |
wantarray ? : |
|
1254
|
0 |
115 |
unless defined $index |
|
1255
|
0 |
115 |
unless exists $self->{$index}{'name'} |
|
1256
|
1 |
114 |
if (defined $new_name) |
|
1258
|
1 |
0 |
if (exists $self->{'data_table'}) { } |
|
|
0 |
0 |
elsif (exists $self->{'column_names'}) { } |
|
1271
|
0 |
24 |
unless defined $index |
|
1272
|
0 |
24 |
unless exists $self->{$index} |
|
1273
|
2 |
22 |
if ($key and $key eq 'name') |
|
1276
|
1 |
21 |
if ($key and defined $value) { } |
|
|
0 |
21 |
elsif ($key and not defined $value) { } |
|
1282
|
0 |
0 |
if (exists $self->{$index}{$key}) { } |
|
1293
|
17 |
4 |
wantarray ? : |
|
1300
|
0 |
0 |
unless defined $index |
|
1301
|
0 |
0 |
if (defined $key) { } |
|
1302
|
0 |
0 |
if (exists $self->{$index}{$key}) |
|
1310
|
0 |
0 |
if $key eq 'name' |
|
1311
|
0 |
0 |
if $key eq 'index' |
|
1319
|
0 |
2 |
unless exists $self->{$source}{'name'} and exists $self->{$target}{'name'} |
|
1323
|
0 |
2 |
if exists $md->{'AUTO'} |
|
1336
|
0 |
187 |
unless $name |
|
1349
|
84 |
515 |
if ($self->{$i}{'name'} =~ /$name/i) |
|
1388
|
0 |
37 |
if @_ |
|
1389
|
12 |
25 |
unless exists $self->{'column_indices'} |
|
1395
|
0 |
118 |
if @_ |
|
1396
|
1 |
117 |
unless exists $self->{'column_indices'} |
|
1402
|
0 |
33 |
if @_ |
|
1403
|
0 |
33 |
unless exists $self->{'column_indices'} |
|
1413
|
0 |
32 |
if @_ |
|
1414
|
5 |
27 |
unless exists $self->{'column_indices'} |
|
1420
|
0 |
72 |
if @_ |
|
1421
|
1 |
71 |
unless exists $self->{'column_indices'} |
|
1427
|
0 |
12 |
if @_ |
|
1428
|
4 |
8 |
unless exists $self->{'column_indices'} |
|
1434
|
0 |
70 |
if @_ |
|
1435
|
0 |
70 |
unless exists $self->{'column_indices'} |
|
1441
|
0 |
0 |
if @_ |
|
1442
|
0 |
0 |
unless exists $self->{'column_indices'} |
|
1457
|
0 |
13 |
unless $row and $row <= $self->{'last_row'} |
|
1458
|
0 |
13 |
unless exists $self->{'SeqFeatureObjects'} |