| line |
true |
false |
branch |
|
35
|
1 |
72 |
if (ref $class) |
|
78
|
0 |
52 |
unless (defined $self->{'data_table'} and ref $self->{'data_table'} eq "ARRAY") |
|
82
|
0 |
0 |
unless $silence |
|
88
|
52 |
0 |
if (defined $self->{'last_row'}) { } |
|
90
|
0 |
52 |
if ($self->{'last_row'} != $number) |
|
104
|
52 |
0 |
if (defined $self->{'number_columns'}) { } |
|
111
|
0 |
945 |
if ($count != $number) |
|
113
|
0 |
0 |
if $count < $number |
|
114
|
0 |
0 |
if $count > $number |
|
124
|
0 |
52 |
if (@problems) |
|
130
|
0 |
0 |
if ($too_low) |
|
131
|
0 |
0 |
unless $silence |
|
135
|
0 |
0 |
if ($too_high) |
|
136
|
0 |
0 |
unless $silence |
|
152
|
0 |
415 |
unless ($self->{$i}{'name'} eq $self->{'data_table'}[0][$i]) |
|
159
|
0 |
0 |
unless $silence |
|
162
|
0 |
415 |
unless ($self->{$i}{'index'} == $i) |
|
164
|
0 |
0 |
unless $silence |
|
168
|
0 |
52 |
if $mdcheck |
|
174
|
6 |
46 |
if ($self->{'gff'}) |
|
180
|
1 |
5 |
if ($self->{'number_columns'} != 9) |
|
186
|
0 |
6 |
if (exists $self->{'0'} and not $self->{'0'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
195
|
0 |
6 |
if (exists $self->{'3'} and not $self->{'3'}{'name'} =~ /start|pos|position/i) |
|
203
|
0 |
6 |
if (exists $self->{'4'} and not $self->{'4'}{'name'} =~ /stop|end|pos|position/i) |
|
211
|
0 |
6 |
if (exists $self->{'6'} and not $self->{'6'}{'name'} =~ /strand/i) |
|
221
|
0 |
6 |
unless ($self->_column_is_integers(3, 4)) |
|
225
|
0 |
6 |
unless ($self->_column_is_numeric(5)) |
|
229
|
0 |
6 |
unless ($self->_column_is_stranded(6)) |
|
235
|
1 |
5 |
if ($gff_check == 0) |
|
242
|
8 |
0 |
if (exists $self->{$i}{'AUTO'}) |
|
246
|
0 |
1 |
unless $silence |
|
251
|
21 |
31 |
if ($self->{'bed'}) |
|
257
|
0 |
21 |
if ($self->{'number_columns'} < 3) |
|
263
|
0 |
21 |
if (exists $self->{'0'} and not $self->{'0'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
271
|
0 |
21 |
if (exists $self->{'1'} and not $self->{'1'}{'name'} =~ /start|pos|position/i) |
|
278
|
0 |
21 |
if (exists $self->{'2'} and not $self->{'2'}{'name'} =~ /stop|end|pos|position/i) |
|
285
|
0 |
21 |
if (exists $self->{'5'} and not $self->{'5'}{'name'} =~ /strand/i) |
|
292
|
0 |
11 |
if (exists $self->{'6'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'6'}{'name'} =~ /start|thick|cds/i) |
|
300
|
0 |
11 |
if (exists $self->{'7'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'7'}{'name'} =~ /end|stop|thick|cds/i) |
|
308
|
0 |
11 |
if (exists $self->{'8'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'8'}{'name'} =~ /item|rgb|color/i) |
|
316
|
0 |
11 |
if (exists $self->{'9'} and not $self->{'format'} =~ /narrow|broad/i and not $self->{'9'}{'name'} =~ /count|number|block|exon/i) |
|
324
|
0 |
21 |
if (exists $self->{'10'} and not $self->{'10'}{'name'} =~ /size|length|block|exon/i) |
|
331
|
0 |
21 |
if (exists $self->{'11'} and not $self->{'11'}{'name'} =~ /start|block|exon/i) |
|
340
|
0 |
21 |
unless ($self->_column_is_integers(1, 2)) |
|
344
|
15 |
6 |
if ($self->{'number_columns'} >= 5) |
|
346
|
0 |
15 |
unless ($self->_column_is_numeric(4)) |
|
351
|
15 |
6 |
if ($self->{'number_columns'} >= 6) |
|
353
|
0 |
15 |
unless ($self->_column_is_stranded(5)) |
|
358
|
4 |
17 |
if ($self->{'format'} and $self->{'format'} =~ /narrow|broad/i) |
|
360
|
0 |
4 |
unless ($self->_column_is_numeric(6, 7, 8)) |
|
365
|
3 |
18 |
if ($self->{'number_columns'} == 12) |
|
367
|
0 |
3 |
unless ($self->_column_is_integers(6, 7, 9)) |
|
371
|
0 |
3 |
unless ($self->_column_is_comma_integers(10, 11)) |
|
376
|
4 |
17 |
if ($self->{'number_columns'} == 15 and $self->{'format'} =~ /gapped/i) |
|
381
|
0 |
4 |
unless ($self->_column_is_integers(6, 7, 9)) |
|
385
|
0 |
4 |
unless ($self->_column_is_comma_integers(10, 11)) |
|
389
|
0 |
4 |
unless ($self->_column_is_numeric(12, 13, 14)) |
|
396
|
0 |
18 |
if ($self->{'format'} and $self->{'format'} =~ /narrowpeak/i and $self->{'number_columns'} != 10) |
|
403
|
0 |
18 |
if ($self->{'format'} and $self->{'format'} =~ /broadpeak/i and $self->{'number_columns'} != 9) |
|
410
|
0 |
18 |
if ($self->{'format'} and $self->{'format'} =~ /gappedpeak/i and $self->{'number_columns'} != 15) |
|
419
|
21 |
0 |
if ($bed_check) { } |
|
433
|
0 |
0 |
if (exists $self->{$i}{'AUTO'}) |
|
437
|
0 |
0 |
unless $silence |
|
442
|
6 |
46 |
if ($self->{'ucsc'}) |
|
449
|
6 |
0 |
if ($colnumber == 16) { } |
|
|
0 |
0 |
elsif ($colnumber == 15 or $colnumber == 12) { } |
|
|
0 |
0 |
elsif ($colnumber == 11) { } |
|
|
0 |
0 |
elsif ($colnumber == 10) { } |
|
455
|
0 |
6 |
unless ($self->{'2'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
460
|
3 |
3 |
unless ($self->{'4'}{'name'} =~ /start|position/i) |
|
464
|
3 |
3 |
unless ($self->{'5'}{'name'} =~ /stop|end|position/i) |
|
468
|
3 |
3 |
unless ($self->{'6'}{'name'} =~ /start|position/i) |
|
472
|
3 |
3 |
unless ($self->{'7'}{'name'} =~ /stop|end|position/i) |
|
476
|
0 |
6 |
unless ($self->_column_is_integers(4, 5, 6, 7, 8)) |
|
480
|
0 |
6 |
unless ($self->_column_is_comma_integers(9, 10)) |
|
484
|
0 |
6 |
unless ($self->_column_is_stranded(3)) |
|
490
|
0 |
0 |
$colnumber == 15 ? : |
|
498
|
0 |
0 |
unless ($self->{'1'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
503
|
0 |
0 |
unless ($self->{'3'}{'name'} =~ /start|position/i) |
|
507
|
0 |
0 |
unless ($self->{'4'}{'name'} =~ /stop|end|position/i) |
|
511
|
0 |
0 |
unless ($self->{'5'}{'name'} =~ /start|position/i) |
|
515
|
0 |
0 |
unless ($self->{'6'}{'name'} =~ /stop|end|position/i) |
|
519
|
0 |
0 |
unless ($self->_column_is_integers(3, 4, 5, 6, 7)) |
|
523
|
0 |
0 |
unless ($self->_column_is_comma_integers(8, 9)) |
|
527
|
0 |
0 |
unless ($self->_column_is_stranded(2)) |
|
536
|
0 |
0 |
unless ($self->{'2'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
541
|
0 |
0 |
unless ($self->{'4'}{'name'} =~ /start|position/i) |
|
545
|
0 |
0 |
unless ($self->{'5'}{'name'} =~ /stop|end|position/i) |
|
549
|
0 |
0 |
unless ($self->{'6'}{'name'} =~ /start|position/i) |
|
553
|
0 |
0 |
unless ($self->{'7'}{'name'} =~ /stop|end|position/i) |
|
557
|
0 |
0 |
unless ($self->_column_is_integers(4, 5, 6, 7, 8)) |
|
561
|
0 |
0 |
unless ($self->_column_is_comma_integers(9, 10)) |
|
565
|
0 |
0 |
unless ($self->_column_is_stranded(3)) |
|
574
|
0 |
0 |
unless ($self->{'1'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
579
|
0 |
0 |
unless ($self->{'3'}{'name'} =~ /start|position/i) |
|
583
|
0 |
0 |
unless ($self->{'4'}{'name'} =~ /stop|end|position/i) |
|
587
|
0 |
0 |
unless ($self->{'5'}{'name'} =~ /start|position/i) |
|
591
|
0 |
0 |
unless ($self->{'6'}{'name'} =~ /stop|end|position/i) |
|
595
|
0 |
0 |
unless ($self->_column_is_integers(3, 4, 5, 6, 7)) |
|
599
|
0 |
0 |
unless ($self->_column_is_comma_integers(8, 9)) |
|
603
|
0 |
0 |
unless ($self->_column_is_stranded(2)) |
|
614
|
3 |
3 |
if ($ucsc_check == 0) |
|
624
|
48 |
0 |
if (exists $self->{$i}{'AUTO'}) |
|
628
|
0 |
3 |
unless $silence |
|
633
|
0 |
52 |
if ($self->{'vcf'}) |
|
639
|
0 |
0 |
if ($self->{'number_columns'} < 8) |
|
645
|
0 |
0 |
unless ($self->{'0'}{'name'} =~ /chrom/i) |
|
649
|
0 |
0 |
if (exists $self->{'1'} and not $self->{'1'}{'name'} =~ /^pos|start/i) |
|
658
|
0 |
0 |
unless ($self->_column_is_integers(1)) |
|
664
|
0 |
0 |
if ($vcf_check) { } |
|
666
|
0 |
0 |
if $self->{'vcf'} == 1 |
|
676
|
0 |
0 |
if (exists $self->{$i}{'AUTO'}) |
|
680
|
0 |
0 |
unless $silence |
|
685
|
0 |
52 |
if (exists $self->{'extension'} and defined $self->{'extension'} and $self->{'extension'} =~ /sgr/i) |
|
693
|
0 |
0 |
if ($self->{'number_columns'} != 3) |
|
697
|
0 |
0 |
unless ($self->{'0'}{'name'} =~ /^#?(?:chr|chromo|seq|refseq|ref_seq|seq|seq_id)/i) |
|
701
|
0 |
0 |
unless ($self->{'1'}{'name'} =~ /start|position/i) |
|
705
|
0 |
0 |
unless ($self->_column_is_integers(1)) |
|
709
|
0 |
0 |
if ($sgr_check == 0) |
|
720
|
0 |
0 |
if (exists $self->{$i}{'AUTO'}) |
|
724
|
0 |
0 |
unless $silence |
|
730
|
29 |
23 |
if ($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)) { } |
|
744
|
18 |
0 |
unless $self->{'headers'} == -1 |
|
756
|
2 |
38 |
if $self->{'last_row'} == 0 |
|
758
|
0 |
101 |
unless exists $self->{$_} |
|
762
|
0 |
1648 |
unless $self->{'data_table'}[$row][$i] =~ /^\d+$/ |
|
772
|
0 |
29 |
if $self->{'last_row'} == 0 |
|
774
|
0 |
45 |
unless exists $self->{$_} |
|
779
|
0 |
407 |
unless $self->{'data_table'}[$row][$i] =~ /^[\d\-\+\.,eE]+$/ |
|
791
|
0 |
13 |
if $self->{'last_row'} == 0 |
|
793
|
0 |
26 |
unless exists $self->{$_} |
|
797
|
0 |
220 |
unless $self->{'data_table'}[$row][$i] =~ /^[\d,]+$/ |
|
806
|
0 |
27 |
unless exists $self->{$index} |
|
808
|
0 |
347 |
unless $self->{'data_table'}[$row][$index] =~ /^(?:\-1|0|1|\+|\-|\.)$/ |
|
821
|
1 |
0 |
if (not defined $_[0]) { } |
|
|
0 |
0 |
elsif ($_[0] eq '0' or $_[0] eq '1') { } |
|
|
0 |
0 |
elsif ($_[0] =~ /[a-zA-Z]+/) { } |
|
841
|
0 |
15 |
unless $self->{'db'} |
|
842
|
0 |
15 |
if $self->{'db'} =~ /^Parsed:/ |
|
843
|
14 |
1 |
if (exists $self->{'db_connection'}) |
|
844
|
14 |
0 |
unless $force |
|
847
|
0 |
1 |
unless $db |
|
861
|
0 |
12 |
unless $dataset |
|
862
|
11 |
1 |
if (exists $self->{'verfied_dataset'}{$dataset}) { } |
|
866
|
0 |
1 |
if ($dataset =~ /^(?:file|http|ftp)/) |
|
877
|
1 |
0 |
if ($verified) |
|
893
|
0 |
2 |
if (ref $self eq "Bio::ToolBox::Data::Stream") |
|
894
|
0 |
0 |
unless ($self->mode) |
|
898
|
0 |
0 |
if (defined $self->{'fh'}) |
|
904
|
0 |
2 |
unless (@_) |
|
914
|
2 |
16 |
if ($i == $deletion_list[0]) { } |
|
930
|
0 |
3 |
if (ref $self eq "Bio::ToolBox::Data::Stream") |
|
931
|
0 |
0 |
unless ($self->mode) |
|
935
|
0 |
0 |
if (defined $self->{'fh'}) |
|
943
|
0 |
3 |
unless (@_) |
|
974
|
2 |
1 |
if exists $self->{'column_indices'} |
|
975
|
0 |
2 |
if ($self->gff or $self->bed or $self->ucsc or $self->vcf) |
|
988
|
20 |
34 |
if (@_) |
|
996
|
0 |
37 |
if @_ |
|
997
|
24 |
13 |
if (defined $self->{'feature_type'}) |
|
1001
|
8 |
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) { } |
|
1019
|
60 |
8 |
if (@_) |
|
1027
|
20 |
26 |
if (@_) |
|
1029
|
0 |
0 |
if (exists $self->{'db_connection'} and $self->{'db_connection'}) |
|
1048
|
72 |
150 |
if (defined $_[0]) |
|
1056
|
5 |
97 |
if (defined $_[0] and $_[0] =~ /^(?:0|1|2|2\.[2|5]|3)$/) |
|
1064
|
43 |
94 |
if (defined $_[0] and $_[0] =~ /^\d+$/) |
|
1072
|
3 |
59 |
if (defined $_[0] and $_[0] =~ /^\d+$/) |
|
1080
|
0 |
44 |
if (defined $_[0] and $_[0] =~ /^[\d\.]+$/) |
|
1088
|
0 |
553 |
if @_ |
|
1094
|
0 |
3 |
if @_ |
|
1100
|
0 |
0 |
if @_ |
|
1106
|
0 |
892 |
if @_ |
|
1112
|
0 |
138 |
if @_ |
|
1118
|
0 |
29 |
if @_ |
|
1124
|
0 |
0 |
if @_ |
|
1130
|
0 |
129 |
if @_ |
|
1149
|
0 |
53 |
unless my $comment = shift() |
|
1158
|
1 |
0 |
if (defined $index) { } |
|
1168
|
0 |
0 |
unless $self->vcf |
|
1169
|
0 |
0 |
if exists $self->{'vcf_headers'} |
|
1173
|
0 |
0 |
if ($comment =~ /^##([\w\-\.]+)=(.+)$/) { } |
|
1181
|
0 |
0 |
if (not $value =~ /^<.+>$/) { } |
|
1200
|
0 |
0 |
unless $self->vcf |
|
1201
|
0 |
0 |
unless exists $self->{'vcf_headers'} |
|
1210
|
0 |
0 |
if $key eq "fileformat" |
|
1211
|
0 |
0 |
if (ref $self->{'vcf_headers'}{$key} eq 'HASH') { } |
|
1239
|
0 |
4 |
if @_ |
|
1244
|
2 |
2 |
wantarray ? : |
|
1250
|
0 |
24 |
unless defined $index |
|
1251
|
0 |
24 |
unless exists $self->{$index}{'name'} |
|
1252
|
1 |
23 |
if (defined $new_name) |
|
1254
|
1 |
0 |
if (exists $self->{'data_table'}) { } |
|
|
0 |
0 |
elsif (exists $self->{'column_names'}) { } |
|
1267
|
0 |
26 |
unless defined $index |
|
1268
|
0 |
26 |
unless exists $self->{$index} |
|
1269
|
2 |
24 |
if ($key and $key eq "name") |
|
1272
|
3 |
21 |
if ($key and defined $value) { } |
|
|
0 |
21 |
elsif ($key and not defined $value) { } |
|
1278
|
0 |
0 |
if (exists $self->{$index}{$key}) { } |
|
1289
|
17 |
4 |
wantarray ? : |
|
1296
|
0 |
0 |
unless defined $index |
|
1297
|
0 |
0 |
if (defined $key) { } |
|
1298
|
0 |
0 |
if (exists $self->{$index}{$key}) |
|
1306
|
0 |
0 |
if $key eq "name" |
|
1307
|
0 |
0 |
if $key eq "index" |
|
1315
|
0 |
2 |
unless exists $self->{$source}{'name'} and exists $self->{$target}{'name'} |
|
1319
|
0 |
2 |
if exists $md->{'AUTO'} |
|
1332
|
0 |
220 |
unless $name |
|
1345
|
88 |
648 |
if ($self->{$i}{'name'} =~ /$name/i) |
|
1370
|
12 |
0 |
unless (defined $coord or defined $chromo or defined $start) |
|
1372
|
12 |
0 |
if (defined $id and defined $self->{'data_table'}[1]) |
|
1373
|
8 |
4 |
if ($self->{'data_table'}[1][$id] =~ /^[\w\-\.]+:\d+(?:[\-\.]{1,2}\d+)?$/) |
|
1378
|
4 |
0 |
if (not defined $coord and defined $name and defined defined $self->{'data_table'}[1]) |
|
1382
|
0 |
4 |
if ($self->{'data_table'}[1][$name] =~ /^[\w\-\.]+:\d+(?:[\-\.]{1,2}\d+)?$/) |
|
1390
|
1 |
17 |
if ($self->{'zerostart'} == 0 and defined $start and substr($self->name($start), -1) eq 0) |
|
1417
|
13 |
13 |
unless exists $self->{'column_indices'} |
|
1418
|
2 |
24 |
if (defined $_[0]) |
|
1419
|
2 |
0 |
if ($_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'}) { } |
|
1431
|
1 |
116 |
unless exists $self->{'column_indices'} |
|
1432
|
2 |
115 |
if (defined $_[0]) |
|
1433
|
2 |
0 |
if ($_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'}) { } |
|
1445
|
0 |
21 |
unless exists $self->{'column_indices'} |
|
1446
|
2 |
19 |
if (defined $_[0]) |
|
1447
|
2 |
0 |
if ($_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'}) { } |
|
1460
|
0 |
109 |
unless exists $self->{'column_indices'} |
|
1461
|
0 |
109 |
if (defined $_[0]) |
|
1462
|
0 |
0 |
if ($_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'}) { } |
|
1474
|
4 |
16 |
unless exists $self->{'column_indices'} |
|
1475
|
2 |
18 |
if (defined $_[0]) |
|
1476
|
2 |
0 |
if ($_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'}) { } |
|
1488
|
1 |
71 |
unless exists $self->{'column_indices'} |
|
1489
|
0 |
72 |
if (defined $_[0]) |
|
1490
|
0 |
0 |
if ($_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'}) { } |
|
1502
|
4 |
10 |
unless exists $self->{'column_indices'} |
|
1503
|
2 |
12 |
if (defined $_[0]) |
|
1504
|
2 |
0 |
if ($_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'}) { } |
|
1516
|
1 |
70 |
unless exists $self->{'column_indices'} |
|
1517
|
0 |
71 |
if (defined $_[0]) |
|
1518
|
0 |
0 |
if ($_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'}) { } |
|
1530
|
0 |
0 |
unless exists $self->{'column_indices'} |
|
1531
|
0 |
0 |
if (defined $_[0]) |
|
1532
|
0 |
0 |
if ($_[0] =~ /^\d+$/ and $_[0] < $self->{'number_columns'}) { } |
|
1545
|
0 |
90 |
if (@_) |
|
1548
|
0 |
0 |
if ($_[0] eq '1' and $n =~ /^start$/i) { } |
|
|
0 |
0 |
elsif ($_[0] eq '0' and $n =~ /^start0$/i) { } |
|
1573
|
0 |
13 |
unless ref $self eq "Bio::ToolBox::Data" |
|
1574
|
0 |
13 |
unless $row and $row <= $self->{'last_row'} |
|
1575
|
0 |
13 |
unless exists $self->{'SeqFeatureObjects'} |