| line |
true |
false |
branch |
|
890
|
2 |
0 |
if (@_) |
|
891
|
1 |
1 |
if ($_[0] =~ /^-/) { } |
|
901
|
2 |
0 |
if ($file) |
|
902
|
0 |
2 |
unless $self->open($file) |
|
914
|
0 |
2 |
unless ($filename) |
|
918
|
0 |
2 |
unless ($filename =~ /\.useq$/i) |
|
922
|
0 |
2 |
if ($self->slices) |
|
930
|
0 |
2 |
unless ($error == 0) |
|
938
|
0 |
2 |
unless $self->_parse_members |
|
947
|
0 |
1 |
unless $self->{'zip'} |
|
951
|
0 |
1 |
unless ($error == 0) |
|
978
|
0 |
7 |
unless my $seq_id = shift() |
|
979
|
7 |
0 |
if (exists $self->{'seq_ids'}{$seq_id}) |
|
990
|
0 |
0 |
unless %{$self->{'metadata'};} |
|
997
|
0 |
1 |
unless $key |
|
998
|
1 |
0 |
unless %{$self->{'metadata'};} |
|
999
|
1 |
0 |
if (exists $self->{'metadata'}{$key}) |
|
1019
|
0 |
1 |
unless my $seq_id = shift() |
|
1021
|
0 |
1 |
unless %{$self->{'metadata'};} |
|
1024
|
0 |
1 |
if (exists $self->{'metadata'}{"chromStats_$seq_id"}) |
|
1049
|
0 |
1 |
unless $self->slice_type($slice) =~ /f/ |
|
1061
|
9151 |
0 |
if (defined $r->[2]) |
|
1065
|
4 |
9147 |
if not defined $min or $r->[2] < $min |
|
1066
|
33 |
9118 |
if not defined $max or $r->[2] > $max |
|
1083
|
1 |
0 |
unless $delay_write |
|
1090
|
0 |
1 |
unless my $seq_id = shift() |
|
1096
|
0 |
0 |
unless my $seq_id = shift() |
|
1104
|
0 |
0 |
unless %{$self->{'metadata'};} |
|
1107
|
0 |
0 |
if (exists $self->{'metadata'}{'globalStats'}) |
|
1130
|
0 |
0 |
if not defined $min or $stats->{'minVal'} < $min |
|
1131
|
0 |
0 |
if not defined $max or $stats->{'maxVal'} > $max |
|
1170
|
0 |
0 |
unless my $slice = shift() |
|
1176
|
0 |
1088 |
unless my $slice = shift() |
|
1182
|
0 |
2021 |
unless my $slice = shift() |
|
1188
|
0 |
4 |
unless my $slice = shift() |
|
1194
|
0 |
1020 |
unless my $slice = shift() |
|
1200
|
0 |
6 |
unless my $slice = shift() |
|
1206
|
0 |
0 |
unless my $slice = shift() |
|
1229
|
0 |
1 |
unless $self->length($seq_id) |
|
1249
|
0 |
2 |
if (ref $args{'-type'} and ref $args{'-type'} eq 'ARRAY') { } |
|
1258
|
0 |
2 |
if ($type =~ /chromosome/) { } |
|
|
2 |
0 |
elsif ($type =~ /region|interval|observation|coverage|wiggle|summary/) { } |
|
1270
|
0 |
0 |
wantarray ? : |
|
1280
|
0 |
2 |
unless $iterator |
|
1283
|
0 |
0 |
if (exists $args{'-iterator'} and $args{'-iterator'}) |
|
1292
|
2 |
0 |
wantarray ? : |
|
1332
|
0 |
0 |
unless @list |
|
1333
|
0 |
0 |
if scalar @list == 1 |
|
1335
|
0 |
0 |
if $f->start == $start and $f->end == $end |
|
1351
|
0 |
3 |
unless $self->length($seq_id) |
|
1357
|
0 |
3 |
if (ref $args{'-type'} and ref $args{'-type'} eq 'ARRAY') { } |
|
1381
|
0 |
1 |
unless $self->length($seq_id) |
|
1386
|
0 |
1 |
unless @slices |
|
1401
|
31 |
0 |
if defined $r->[2] |
|
1405
|
1 |
0 |
wantarray ? : |
|
1413
|
0 |
0 |
unless $self->length($seq_id) |
|
1418
|
0 |
0 |
unless @slices |
|
1432
|
0 |
0 |
wantarray ? : |
|
1445
|
0 |
1 |
unless ($readMe) |
|
1454
|
0 |
5 |
if (/^#/) |
|
1455
|
0 |
0 |
unless $_ =~ /validCount/ |
|
1458
|
5 |
0 |
if (/^\s*([^=\s]+)\s*=\s*(.+)\s*$/) |
|
1479
|
2 |
6 |
if $member eq "archiveReadMe.txt" |
|
1486
|
0 |
6 |
unless ($chromo and $strand and defined $start and defined $stop and $number and $extension) |
|
1493
|
2 |
4 |
unless (defined $self->{'stranded'}) |
|
1494
|
1 |
1 |
if ($strand eq '.') { } |
|
1505
|
3 |
3 |
if (exists $self->{'seq_ids'}{$chromo}) { } |
|
1506
|
3 |
0 |
if ($stop > $self->{'seq_ids'}{$chromo}) |
|
1515
|
1 |
0 |
$strand eq '-' ? : |
|
|
4 |
1 |
$strand eq '.' ? : |
|
|
1 |
5 |
$strand eq '+' ? : |
|
1520
|
0 |
6 |
if ($start >= $stop) |
|
1535
|
0 |
2 |
if (@errors) |
|
1538
|
0 |
2 |
unless (%{$self->{'coord2file'};}) |
|
1551
|
5 |
0 |
if ($_[0] =~ /^\-/) { } |
|
1561
|
0 |
5 |
unless ($seq_id) |
|
1575
|
0 |
6 |
unless exists $self->{'coord2file'}{$seq_id} |
|
1579
|
6 |
0 |
if ($strand == 0) { } |
|
1582
|
1 |
5 |
if $self->stranded |
|
1587
|
0 |
0 |
unless $self->stranded |
|
1592
|
1 |
5 |
if ($both) { } |
|
1618
|
4 |
1 |
unless exists $wanted{$_} |
|
1625
|
1009 |
7 |
if exists $self->{'buffer'}{$slice} |
|
1634
|
0 |
7 |
if ($type eq 's') { } |
|
|
0 |
7 |
elsif ($type eq 'sf') { } |
|
|
0 |
7 |
elsif ($type eq 'st') { } |
|
|
0 |
7 |
elsif ($type eq 'ss') { } |
|
|
6 |
1 |
elsif ($type eq 'ssf') { } |
|
|
0 |
1 |
elsif ($type eq 'sst') { } |
|
|
1 |
0 |
elsif ($type eq 'ssft') { } |
|
|
0 |
0 |
elsif ($type eq 'i') { } |
|
|
0 |
0 |
elsif ($type eq 'if') { } |
|
|
0 |
0 |
elsif ($type eq 'it') { } |
|
|
0 |
0 |
elsif ($type eq 'ii') { } |
|
|
0 |
0 |
elsif ($type eq 'iif') { } |
|
|
0 |
0 |
elsif ($type eq 'iit') { } |
|
|
0 |
0 |
elsif ($type eq 'iift') { } |
|
|
0 |
0 |
elsif ($type eq 'is') { } |
|
|
0 |
0 |
elsif ($type eq 'isf') { } |
|
|
0 |
0 |
elsif ($type eq 'ist') { } |
|
|
0 |
0 |
elsif ($type eq 'isft') { } |
|
2172
|
0 |
1000 |
unless @$slices |
|
2178
|
0 |
1001 |
unless $self->slice_type($slice) =~ /f/ |
|
2191
|
1000 |
0 |
$count ? : |
|
2197
|
0 |
10 |
unless @$slices |
|
2208
|
0 |
11 |
unless $self->slice_type($slice) =~ /f/ |
|
2218
|
11994 |
0 |
if (defined $r->[2]) |
|
2222
|
40 |
11954 |
if not defined $min or $r->[2] < $min |
|
2223
|
111 |
11883 |
if not defined $max or $r->[2] > $max |
|
2241
|
0 |
1 |
unless -w $self->zip->fileName |
|
2247
|
1 |
0 |
if exists $md->{'comments'} |
|
2253
|
5 |
2 |
if /useqArchiveVersion|dataType|versionedGenome|comments|chromStats|globalStats/ |
|
2260
|
0 |
1 |
if exists $md->{'globalStats'} |
|
2262
|
1 |
6 |
if /chromStats/ |
|
2277
|
0 |
2 |
unless $score->{'validCount'} |
|
2283
|
0 |
1 |
unless $score->{'validCount'} |
|
2285
|
1 |
0 |
if ($score->{'validCount'} > 1) |
|
2288
|
0 |
1 |
if $var < 0 |
|
2321
|
0 |
0 |
unless exists $self->{'useq'} |
|
2327
|
0 |
0 |
unless exists $self->{'useq'} |
|
2333
|
0 |
0 |
unless exists $self->{'useq'} |
|
2339
|
0 |
0 |
unless exists $self->{'useq'} |
|
2345
|
0 |
0 |
unless exists $self->{'useq'} |
|
2351
|
0 |
0 |
unless exists $self->{'useq'} |
|
2365
|
1 |
0 |
if exists $args{'-useq'} |
|
2412
|
0 |
0 |
wantarray ? : |
|
2455
|
0 |
4 |
unless my $useq = $args{'-useq'} |
|
2470
|
3 |
1 |
if (scalar @slices > 1) |
|
2479
|
2 |
2 |
if ($iterator->type =~ /region|interval|observation/) |
|
2493
|
1 |
1 |
$iterator->type =~ /summary/ ? : |
|
2497
|
0 |
2 |
if ($iterator->strand == 0 and $useq->stranded) { } |
|
2502
|
0 |
0 |
if ($useq->slice_strand($_) == 1) { } |
|
2518
|
1 |
1 |
if ($iterator->type =~ /:(\d+)$/i) |
|
2521
|
0 |
1 |
if $bin > $length |
|
2533
|
2 |
8 |
if ($self->{'wiggle'} == 1) { } |
|
|
2 |
6 |
elsif ($self->{'wiggle'} == 2) { } |
|
2553
|
2 |
4 |
unless ($self->{'current_results'}) |
|
2555
|
0 |
2 |
unless $slice |
|
2562
|
0 |
291 |
unless $Bio::DB::USeq::Iterator::a->[0] <=> $Bio::DB::USeq::Iterator::b->[0] |
|
2569
|
0 |
6 |
unless (defined $obs) |
|
2578
|
5 |
1 |
defined $obs->[3] ? : |
|
2595
|
1 |
1 |
unless $slices |
|
2604
|
1 |
0 |
if ($self->{'bin'} and $step > 1) { } |
|
2616
|
1000 |
0 |
if (scalar @$slices > 1) { } |
|
2621
|
939 |
1061 |
if $s > $useq->slice_end($slice) |
|
2622
|
60 |
1001 |
if $e < $useq->slice_start($slice) |
|
2656
|
0 |
0 |
exists $pos2score{$s} ? : |
|
2664
|
0 |
1 |
$strand == -1 ? : |
|
|
0 |
1 |
$strand == 1 ? : |
|
2684
|
1 |
1 |
unless $slices |
|
2702
|
0 |
1 |
$strand == -1 ? : |
|
|
0 |
1 |
$strand == 1 ? : |
|
2716
|
0 |
1 |
unless my $useq = $args{'-useq'} |
|
2725
|
1 |
0 |
wantarray ? : |
|
2752
|
0 |
0 |
if $bins and $bins > 1 |
|
2764
|
0 |
0 |
unless defined $s |
|
2767
|
0 |
0 |
if not defined $min or $s < $min |
|
2768
|
0 |
0 |
if not defined $max or $s > $max |
|
2805
|
0 |
1 |
unless my $useq = $args{'-useq'} |
|
2808
|
1 |
0 |
if exists $args{'-slices'} |
|
2809
|
1 |
0 |
if exists $args{'-bin'} |
|
2810
|
1 |
0 |
if exists $args{'-step'} |
|
2820
|
1 |
0 |
if exists $self->{'bin'} |
|
2822
|
1 |
0 |
if exists $self->{'step'} |
|
2826
|
1 |
0 |
if exists $self->{'slices'} |
|
2827
|
0 |
1 |
unless ($slices) |
|
2845
|
10 |
0 |
if (scalar @$slices > 1) { } |
|
2850
|
0 |
20 |
if $s > $useq->slice_end($slice) |
|
2851
|
9 |
11 |
if $e < $useq->slice_start($slice) |