| 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 |
8 |
unless my $seq_id = shift()
|
|
979
|
8 |
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"})
|
|
1045
|
1 |
0 |
unless $delay_write
|
|
1052
|
0 |
1 |
unless my $seq_id = shift()
|
|
1058
|
0 |
0 |
unless my $seq_id = shift()
|
|
1066
|
0 |
0 |
unless %{$self->{'metadata'};}
|
|
1069
|
0 |
0 |
if (exists $self->{'metadata'}{'globalStats'})
|
|
1092
|
0 |
0 |
if not defined $min or $stats->{'minVal'} < $min
|
|
1093
|
0 |
0 |
if not defined $max or $stats->{'maxVal'} < $max
|
|
1132
|
0 |
0 |
unless my $slice = shift()
|
|
1138
|
0 |
1087 |
unless my $slice = shift()
|
|
1144
|
0 |
2020 |
unless my $slice = shift()
|
|
1150
|
0 |
4 |
unless my $slice = shift()
|
|
1156
|
0 |
1020 |
unless my $slice = shift()
|
|
1162
|
0 |
6 |
unless my $slice = shift()
|
|
1168
|
0 |
0 |
unless my $slice = shift()
|
|
1191
|
0 |
1 |
unless $self->length($seq_id)
|
|
1211
|
0 |
2 |
if (ref $args{'-type'} and ref $args{'-type'} eq 'ARRAY') { }
|
|
1220
|
0 |
2 |
if ($type =~ /chromosome/) { }
|
|
|
2 |
0 |
elsif ($type =~ /region|interval|observation|coverage|wiggle|summary/) { }
|
|
1232
|
0 |
0 |
wantarray ? :
|
|
1242
|
0 |
2 |
unless $iterator
|
|
1245
|
0 |
0 |
if (exists $args{'-iterator'} and $args{'-iterator'})
|
|
1254
|
2 |
0 |
wantarray ? :
|
|
1294
|
0 |
0 |
unless @list
|
|
1295
|
0 |
0 |
if scalar @list == 1
|
|
1297
|
0 |
0 |
if $f->start == $start and $f->end == $end
|
|
1313
|
0 |
3 |
unless $self->length($seq_id)
|
|
1319
|
0 |
3 |
if (ref $args{'-type'} and ref $args{'-type'} eq 'ARRAY') { }
|
|
1343
|
0 |
1 |
unless $self->length($seq_id)
|
|
1348
|
0 |
1 |
unless @slices
|
|
1363
|
31 |
0 |
if defined $r->[2]
|
|
1367
|
1 |
0 |
wantarray ? :
|
|
1375
|
0 |
0 |
unless $self->length($seq_id)
|
|
1380
|
0 |
0 |
unless @slices
|
|
1394
|
0 |
0 |
wantarray ? :
|
|
1407
|
0 |
1 |
unless ($readMe)
|
|
1416
|
0 |
5 |
if (/^#/)
|
|
1417
|
0 |
0 |
unless $_ =~ /validCount/
|
|
1420
|
5 |
0 |
if (/^\s*([^=\s]+)\s*=\s*(.+)\s*$/)
|
|
1441
|
2 |
6 |
if $member eq 'archiveReadMe.txt'
|
|
1448
|
0 |
6 |
unless ($chromo and $strand and defined $start and defined $stop and $number and $extension)
|
|
1455
|
2 |
4 |
unless (defined $self->{'stranded'})
|
|
1456
|
1 |
1 |
if ($strand eq '.') { }
|
|
1467
|
3 |
3 |
if (exists $self->{'seq_ids'}{$chromo}) { }
|
|
1468
|
3 |
0 |
if ($stop > $self->{'seq_ids'}{$chromo})
|
|
1477
|
1 |
0 |
$strand eq '-' ? :
|
|
|
4 |
1 |
$strand eq '.' ? :
|
|
|
1 |
5 |
$strand eq '+' ? :
|
|
1490
|
0 |
2 |
if (@errors)
|
|
1493
|
0 |
2 |
unless (%{$self->{'coord2file'};})
|
|
1506
|
5 |
0 |
if ($_[0] =~ /^\-/) { }
|
|
1516
|
0 |
5 |
unless ($seq_id)
|
|
1530
|
0 |
6 |
unless exists $self->{'coord2file'}{$seq_id}
|
|
1534
|
6 |
0 |
if ($strand == 0) { }
|
|
1537
|
1 |
5 |
if $self->stranded
|
|
1542
|
0 |
0 |
unless $self->stranded
|
|
1547
|
1 |
5 |
if ($both) { }
|
|
1573
|
4 |
1 |
unless exists $wanted{$_}
|
|
1580
|
1009 |
7 |
if exists $self->{'buffer'}{$slice}
|
|
1589
|
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') { }
|
|
2127
|
0 |
1000 |
unless @$slices
|
|
2133
|
0 |
1001 |
unless $self->slice_type($slice) =~ /f/
|
|
2146
|
1000 |
0 |
$count ? :
|
|
2152
|
0 |
11 |
unless @$slices
|
|
2163
|
0 |
12 |
unless $self->slice_type($slice) =~ /f/
|
|
2173
|
21145 |
0 |
if (defined $r->[2])
|
|
2177
|
44 |
21101 |
if not defined $min or $r->[2] < $min
|
|
2178
|
144 |
21001 |
if not defined $max or $r->[2] > $max
|
|
2196
|
0 |
1 |
unless -w $self->zip->fileName
|
|
2202
|
1 |
0 |
if exists $md->{'comments'}
|
|
2208
|
5 |
2 |
if /useqArchiveVersion|dataType|versionedGenome|comments|chromStats|globalStats/
|
|
2215
|
0 |
1 |
if exists $md->{'globalStats'}
|
|
2217
|
1 |
6 |
if /chromStats/
|
|
2232
|
0 |
2 |
unless $score->{'validCount'}
|
|
2238
|
0 |
1 |
unless $score->{'validCount'}
|
|
2240
|
1 |
0 |
if ($score->{'validCount'} > 1)
|
|
2243
|
0 |
1 |
if $var < 0
|
|
2276
|
0 |
0 |
unless exists $self->{'useq'}
|
|
2282
|
0 |
0 |
unless exists $self->{'useq'}
|
|
2288
|
0 |
0 |
unless exists $self->{'useq'}
|
|
2294
|
0 |
0 |
unless exists $self->{'useq'}
|
|
2300
|
0 |
0 |
unless exists $self->{'useq'}
|
|
2306
|
0 |
0 |
unless exists $self->{'useq'}
|
|
2320
|
1 |
0 |
if exists $args{'-useq'}
|
|
2367
|
0 |
0 |
wantarray ? :
|
|
2410
|
0 |
4 |
unless my $useq = $args{'-useq'}
|
|
2425
|
3 |
1 |
if (scalar @slices > 1)
|
|
2434
|
2 |
2 |
if ($iterator->type =~ /region|interval|observation/)
|
|
2448
|
1 |
1 |
$iterator->type =~ /summary/ ? :
|
|
2452
|
0 |
2 |
if ($iterator->strand == 0 and $useq->stranded) { }
|
|
2457
|
0 |
0 |
if ($useq->slice_strand($_) == 1) { }
|
|
2473
|
1 |
1 |
if ($iterator->type =~ /:(\d+)$/i)
|
|
2476
|
0 |
1 |
if $bin > $length
|
|
2488
|
2 |
8 |
if ($self->{'wiggle'} == 1) { }
|
|
|
2 |
6 |
elsif ($self->{'wiggle'} == 2) { }
|
|
2508
|
2 |
4 |
unless ($self->{'current_results'})
|
|
2510
|
0 |
2 |
unless $slice
|
|
2517
|
0 |
291 |
unless $Bio::DB::USeq::Iterator::a->[0] <=> $Bio::DB::USeq::Iterator::b->[0]
|
|
2524
|
0 |
6 |
unless (defined $obs)
|
|
2533
|
5 |
1 |
defined $obs->[3] ? :
|
|
2550
|
1 |
1 |
unless $slices
|
|
2559
|
1 |
0 |
if ($self->{'bin'} and $step > 1) { }
|
|
2571
|
1000 |
0 |
if (scalar @$slices > 1) { }
|
|
2576
|
939 |
1061 |
if $s > $useq->slice_end($slice)
|
|
2577
|
60 |
1001 |
if $e < $useq->slice_start($slice)
|
|
2611
|
0 |
0 |
exists $pos2score{$s} ? :
|
|
2619
|
0 |
1 |
$strand == -1 ? :
|
|
|
0 |
1 |
$strand == 1 ? :
|
|
2639
|
1 |
1 |
unless $slices
|
|
2657
|
0 |
1 |
$strand == -1 ? :
|
|
|
0 |
1 |
$strand == 1 ? :
|
|
2671
|
0 |
1 |
unless my $useq = $args{'-useq'}
|
|
2680
|
1 |
0 |
wantarray ? :
|
|
2707
|
0 |
0 |
if $bins and $bins > 1
|
|
2719
|
0 |
0 |
unless defined $s
|
|
2722
|
0 |
0 |
if not defined $min or $s < $min
|
|
2723
|
0 |
0 |
if not defined $max or $s > $max
|
|
2760
|
0 |
1 |
unless my $useq = $args{'-useq'}
|
|
2763
|
1 |
0 |
if exists $args{'-slices'}
|
|
2764
|
1 |
0 |
if exists $args{'-bin'}
|
|
2765
|
1 |
0 |
if exists $args{'-step'}
|
|
2775
|
1 |
0 |
if exists $self->{'bin'}
|
|
2777
|
1 |
0 |
if exists $self->{'step'}
|
|
2781
|
1 |
0 |
if exists $self->{'slices'}
|
|
2782
|
0 |
1 |
unless ($slices)
|
|
2800
|
10 |
0 |
if (scalar @$slices > 1) { }
|
|
2805
|
0 |
20 |
if $s > $useq->slice_end($slice)
|
|
2806
|
9 |
11 |
if $e < $useq->slice_start($slice)
|