| 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) |
|
130
|
0 |
0 |
if $Taste->ucsc == 10 |
|
133
|
0 |
0 |
if ($Taste->ucsc == 10) |
|
141
|
0 |
0 |
if $Taste->ucsc == 11 |
|
144
|
0 |
0 |
if ($Taste->ucsc == 11) |
|
152
|
0 |
0 |
if ($Taste->ucsc == 12) |
|
157
|
0 |
0 |
if ($Taste->bed == 12) |
|
162
|
0 |
0 |
if ($Taste->ucsc == 12) |
|
167
|
0 |
0 |
if ($Taste->bed == 12) |
|
175
|
0 |
0 |
if ($Taste->ucsc == 15) |
|
180
|
0 |
0 |
if ($Taste->ucsc == 15) |
|
188
|
0 |
3 |
if ($Taste->ucsc == 16) |
|
191
|
0 |
3 |
if $Taste->ucsc == 16 |
|
194
|
3 |
0 |
if ($Taste->ucsc == 16) |
|
203
|
0 |
11 |
unless $file =~ /\.g[tf]f\d?(?:\.gz)?$/i |
|
204
|
0 |
11 |
unless my $fh = $self->open_to_read_fh($file) |
|
208
|
11 |
1277 |
unless my $line = $fh->getline |
|
209
|
0 |
1277 |
unless $line =~ /\w+/ |
|
210
|
36 |
1241 |
if $line =~ /^#/ |
|
226
|
60 |
0 |
if (exists $self->{'fh'} and $self->{'fh'}) { } |
|
|
0 |
0 |
elsif ($self->filename) { } |
|
237
|
0 |
60 |
if ($self->last_row != 0 or $self->number_columns != 0) |
|
253
|
0 |
60 |
if ($line2 =~ /[\r\n]+/) |
|
269
|
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) { } |
|
334
|
8 |
0 |
if ($line =~ /type=(\w+)/i) |
|
351
|
0 |
60 |
if ($self->_commented_header_line($line)) |
|
364
|
5 |
55 |
if ($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) { } |
|
392
|
13 |
47 |
unless ($self->number_columns) |
|
403
|
77 |
60 |
if ($self->number_columns == 0) { } |
|
413
|
0 |
0 |
if ($self->number_columns == 0 and scalar @{$self->{'comments'};} and $self->{'comments'}[-1] =~ /\t/) |
|
423
|
0 |
0 |
if ($noheader and not $self->bed and not $self->gff and not $self->vcf and not $self->ucsc) |
|
446
|
60 |
0 |
if ($nextline) |
|
448
|
0 |
60 |
if (scalar(@nextdata) - 1 == $self->number_columns) |
|
457
|
26 |
34 |
if (ref $self eq "Bio::ToolBox::Data::Stream") |
|
469
|
60 |
0 |
if $fh |
|
492
|
0 |
574 |
if (index($linedata[-1], "\t") != -1) |
|
506
|
0 |
70 |
unless defined $filename |
|
508
|
0 |
70 |
unless ($extension) |
|
510
|
0 |
0 |
if ($filename =~ /(\.\w+(?:\.gz)?)$/i) |
|
528
|
7 |
1 |
if (scalar @_ == 1) { } |
|
536
|
8 |
0 |
unless (exists $args{'gz'}) |
|
539
|
0 |
8 |
unless ($self->verify) |
|
545
|
0 |
8 |
unless ($args{'filename'} or $self->filename) |
|
555
|
0 |
8 |
if ($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 $extension) { } |
|
556
|
0 |
0 |
unless ($self->gff) |
|
558
|
0 |
0 |
$extension =~ /gtf/i ? : |
|
559
|
0 |
0 |
unless ($self->verify and $self->gff) |
|
566
|
1 |
2 |
unless ($self->bed) |
|
569
|
0 |
1 |
unless ($self->verify and $self->bed) |
|
571
|
0 |
0 |
$extension =~ /gz$/i ? : |
|
576
|
0 |
0 |
unless ($self->vcf) |
|
579
|
0 |
0 |
unless ($self->verify and $self->vcf) |
|
581
|
0 |
0 |
$extension =~ /gz$/i ? : |
|
586
|
0 |
0 |
unless ($self->{'extension'} =~ /sgr/i) |
|
592
|
0 |
0 |
if ($self->extension =~ /txt/) |
|
599
|
0 |
0 |
if ($self->ucsc != $self->number_columns) |
|
603
|
0 |
0 |
unless ($self->verify and $self->ucsc) |
|
605
|
0 |
0 |
$extension =~ /gz$/i ? : |
|
612
|
5 |
0 |
unless $self->{'headers'} == -1 |
|
618
|
0 |
0 |
if ($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) { } |
|
619
|
0 |
0 |
$self->gff == 2.5 ? : |
|
|
0 |
0 |
$self->gff == 3 ? : |
|
622
|
0 |
0 |
if ($self->format) { } |
|
|
0 |
0 |
elsif ($self->number_columns == 4 and $self->name(3) =~ /score/i) { } |
|
637
|
0 |
0 |
if ($self->format) { } |
|
661
|
0 |
0 |
if ($self->extension =~ /g[tf]f/i) { } |
|
|
0 |
0 |
elsif ($self->extension =~ /bed|bdg|peak/i) { } |
|
662
|
0 |
0 |
$self->gff ? : |
|
665
|
0 |
0 |
$self->bed ? : |
|
683
|
8 |
0 |
unless ($args{'format'}) |
|
684
|
0 |
8 |
if (defined $args{'simple'}) { } |
|
|
8 |
0 |
elsif ($extension) { } |
|
690
|
0 |
8 |
if ($extension =~ /sgr|cdt/i) { } |
|
706
|
8 |
0 |
unless (defined $args{'gz'}) |
|
709
|
0 |
8 |
if ($extension =~ /\.vcf\.gz/i) { } |
|
|
0 |
8 |
elsif ($extension =~ /\.gz$/i) { } |
|
722
|
0 |
8 |
if ($args{'gz'} and not $extension =~ /\.gz$/i) { } |
|
|
0 |
8 |
elsif (not $args{'gz'} and $extension =~ /\.gz$/i) { } |
|
732
|
0 |
8 |
if (length $name . $extension > 255) |
|
744
|
0 |
0 |
if (defined $strand_i and $self->gff || $self->bed || $self->ucsc) |
|
746
|
0 |
0 |
if ($self->gff) { } |
|
|
0 |
0 |
elsif ($self->bed or $self->ucsc) { } |
|
749
|
0 |
0 |
if ($s =~ /\d/) |
|
750
|
0 |
0 |
$s == -1 ? : |
|
|
0 |
0 |
$s == 1 ? : |
|
758
|
0 |
0 |
if ($s =~ /\d/) |
|
759
|
0 |
0 |
$s >= 0 ? : |
|
769
|
0 |
8 |
unless defined $fh |
|
773
|
8 |
0 |
if ($args{'format'} eq "text") |
|
777
|
0 |
8 |
if ($self->gff) |
|
782
|
5 |
0 |
unless ($self->gff or $self->bed or $self->ucsc or $self->vcf or $extension =~ /sgr|kgg|cdt|peak/i) |
|
788
|
0 |
5 |
if ($self->program) |
|
791
|
5 |
0 |
if ($self->database) |
|
794
|
5 |
0 |
if ($self->feature) |
|
803
|
4 |
2 |
unless (/\n$/s) |
|
808
|
5 |
1 |
if (/^#/) { } |
|
828
|
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) { } |
|
854
|
0 |
0 |
if $_ eq "name" |
|
855
|
0 |
0 |
if $_ eq "index" |
|
856
|
0 |
0 |
if $_ eq "AUTO" |
|
870
|
5 |
3 |
if ($self->{'headers'} == 1) |
|
876
|
0 |
8 |
if ($args{'format'} eq 'simple') { } |
|
885
|
0 |
0 |
if ($_ eq '.') { } |
|
922
|
120 |
41 |
ref($self) =~ /^Bio::ToolBox/ ? : |
|
925
|
120 |
41 |
if (not $file and $obj) |
|
928
|
0 |
161 |
unless ($file) |
|
935
|
0 |
161 |
if ($file =~ /\.gz$/i) { } |
|
|
0 |
161 |
elsif ($file =~ /\.bz2$/i) { } |
|
937
|
0 |
0 |
unless $fh = "IO::File"->new("gzip -dc $file |") |
|
942
|
0 |
0 |
unless $fh = "IO::File"->new("bzip2 -dc $file |") |
|
947
|
0 |
161 |
unless $fh = "IO::File"->new($file, "r") |
|
951
|
120 |
41 |
if ($obj) |
|
963
|
0 |
10 |
unless ($filename) |
|
971
|
0 |
10 |
if (length $name > 255) |
|
977
|
2 |
8 |
unless (defined $gz) |
|
980
|
0 |
2 |
if ($filename =~ /\.vcf(\.gz)?$/i) { } |
|
|
0 |
2 |
elsif ($filename =~ /\.gz$/i) { } |
|
992
|
0 |
10 |
if ($gz == 1 and not $gzip_app) { } |
|
|
0 |
20 |
elsif ($gz == 2 and not $bgzip_app) { } |
|
996
|
0 |
0 |
if ($gzip_app) { } |
|
1004
|
0 |
0 |
unless ($gzip_app) |
|
1012
|
0 |
0 |
if ($bgzip_app) |
|
1017
|
0 |
0 |
unless ($bgzip_app) |
|
1021
|
0 |
10 |
$gz == 2 ? : |
|
|
0 |
10 |
$gz == 1 ? : |
|
1024
|
8 |
2 |
unless (defined $append) |
|
1032
|
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) { } |
|
1033
|
0 |
8 |
unless $fh = "IO::File"->new($filename, "w") |
|
1037
|
0 |
0 |
unless $fh = "IO::File"->new("| $gzipper >$filename") |
|
1041
|
0 |
2 |
unless $fh = "IO::File"->new(">> $filename") |
|
1045
|
0 |
0 |
unless $fh = "IO::File"->new("| $gzipper >>$filename") |
|
1048
|
10 |
0 |
if defined $fh |
|
1057
|
60 |
0 |
if (-e $filename) { } |
|
1066
|
0 |
0 |
if (-e $filename . $ext) |
|
1078
|
192 |
0 |
if exists $self->{'fh'} |
|
1084
|
70 |
0 |
if exists $self->{'fh'} and $self->{'fh'} |
|
1094
|
30 |
30 |
if (scalar @{$data->{'comments'};} >= 1) |
|
1101
|
0 |
60 |
if (scalar @commentdata == scalar @linedata) { } |
|
1122
|
0 |
0 |
if ($key eq "index") |
|
1123
|
0 |
0 |
if ($index != $value) |
|
1135
|
0 |
0 |
unless (exists $temphash{'index'}) |
|
1141
|
0 |
0 |
if (exists $data->{$index}) { } |
|
1167
|
0 |
5 |
if (not $self->gff or $force) |
|
1168
|
0 |
0 |
if (defined $version) { } |
|
|
0 |
0 |
elsif ($self->extension =~ /gtf/i) { } |
|
|
0 |
0 |
elsif ($self->extension =~ /gff3/i) { } |
|
1182
|
5 |
0 |
unless ($self->format) |
|
1184
|
0 |
0 |
$v > 2 ? : |
|
|
5 |
0 |
$v == 3 ? : |
|
1195
|
45 |
0 |
if ($force or not exists $self->{$i}) |
|
1201
|
45 |
0 |
if ($force or not defined $self->{'column_names'}[$i]) |
|
1208
|
5 |
0 |
if ($force or $self->{'number_columns'} == 0) |
|
1213
|
5 |
0 |
unless $self->{'0'}{'name'} =~ /^#/ |
|
1216
|
5 |
0 |
unless (defined $self->{'feature'}) |
|
1241
|
0 |
27 |
if ($self->format =~ /bedgraph/i or $self->extension =~ /bg|bdg|graph/i) { } |
|
1260
|
200 |
0 |
if ($force or not exists $self->{$i}) |
|
1266
|
200 |
0 |
if ($force or not defined $self->{'column_names'}[$i]) |
|
1273
|
27 |
0 |
unless (defined $self->{'feature'}) |
|
1278
|
27 |
0 |
unless $self->{'0'}{'name'} =~ /^#/ |
|
1293
|
8 |
8 |
if ($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 $self->extension =~ /gapped/i) { } |
|
1318
|
200 |
0 |
if ($force or not exists $self->{$i}) |
|
1324
|
200 |
0 |
if ($force or not defined $self->{'column_names'}[$i]) |
|
1331
|
16 |
0 |
unless (defined $self->{'feature'}) |
|
1336
|
16 |
0 |
unless $self->{'0'}{'name'} =~ /^#/ |
|
1357
|
3 |
0 |
if ($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) { } |
|
1383
|
48 |
0 |
if ($force or not exists $self->{$i}) |
|
1389
|
48 |
0 |
if ($force or not defined $self->{'column_names'}[$i]) |
|
1396
|
3 |
0 |
unless (defined $self->{'feature'}) |
|
1401
|
3 |
0 |
unless $self->{'0'}{'name'} =~ /^#/ |
|
1419
|
0 |
0 |
if ($force or not exists $self->{$i}) |
|
1425
|
0 |
0 |
if ($force or not defined $self->{'column_names'}[$i]) |
|
1434
|
0 |
0 |
unless $self->{'0'}{'name'} =~ /^#/ |
|
1437
|
0 |
0 |
unless (defined $self->{'feature'}) |
|
1457
|
0 |
68 |
if (exists $self->{$i}) { } |
|
1458
|
0 |
0 |
unless ($namelist[$i] eq $self->{$i}{'name'}) |
|
1476
|
13 |
0 |
if (scalar @namelist != $self->{'number_columns'}) |
|
1495
|
5 |
46 |
if ($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') { } |