| line |
true |
false |
branch |
|
46
|
0 |
0 |
unless $type eq 'bam' or $type eq 'bed'
|
|
49
|
0 |
0 |
unless my $genomeCoverageBed = can_run('genomeCoverageBed')
|
|
51
|
0 |
0 |
unless my $bedGraphToBigWig = can_run('bedGraphToBigWig')
|
|
53
|
0 |
0 |
unless my $awk = can_run('awk')
|
|
56
|
0 |
0 |
if (defined $log)
|
|
57
|
0 |
0 |
unless open LOG, '>>', $log
|
|
63
|
0 |
0 |
unless -e $infile
|
|
65
|
0 |
0 |
unless -d $dest
|
|
67
|
0 |
0 |
unless -e $chromsizes
|
|
70
|
0 |
0 |
if ($want_norm == 1)
|
|
72
|
0 |
0 |
if defined $log
|
|
79
|
0 |
0 |
if ($strand eq '+') { }
|
|
87
|
0 |
0 |
if ($type eq 'bed') { }
|
|
91
|
0 |
0 |
if ($strand eq '-') { }
|
|
99
|
0 |
0 |
if (defined $log)
|
|
104
|
0 |
0 |
unless ($success)
|
|
110
|
0 |
0 |
if (defined $log)
|
|
121
|
0 |
0 |
unless my $bed2bigBed = can_run('bedToBigBed')
|
|
124
|
0 |
0 |
if (defined $log)
|
|
125
|
0 |
0 |
unless open LOG, '>>', $log
|
|
129
|
0 |
0 |
unless -e $infile
|
|
131
|
0 |
0 |
unless -e $chromsizes
|
|
133
|
0 |
0 |
unless -d $dest
|
|
141
|
0 |
0 |
if (defined $log)
|
|
145
|
0 |
0 |
unless ($success)
|
|
152
|
0 |
0 |
if (defined $log)
|
|
161
|
0 |
0 |
unless my $bedtools = can_run('bedtools')
|
|
164
|
0 |
0 |
unless -e $infile
|
|
166
|
0 |
0 |
unless -d $dest
|
|
168
|
0 |
0 |
unless open LOG, '>>', $log
|
|
|
0 |
0 |
if (defined $log)
|
|
172
|
0 |
0 |
if (defined $log)
|
|
175
|
0 |
0 |
unless ($success)
|
|
182
|
0 |
0 |
if ($rm_orig)
|
|
183
|
0 |
0 |
unless unlink $infile
|
|
185
|
0 |
0 |
if (defined $log)
|
|
190
|
0 |
0 |
if (defined $log)
|
|
251
|
0 |
0 |
if $d > 0 or $u > 0 or not $e
|
|
252
|
0 |
0 |
if ($strand eq '+') { }
|
|
|
0 |
0 |
elsif ($strand eq '-') { }
|
|
253
|
0 |
0 |
if ($d > 0)
|
|
257
|
0 |
0 |
if ($u > 0)
|
|
265
|
0 |
0 |
if ($u > 0)
|
|
269
|
0 |
0 |
if ($d > 0)
|
|
276
|
0 |
0 |
if ($right - $width <= 0) { }
|
|
282
|
0 |
0 |
if ($left - $width <= 0) { }
|
|
288
|
0 |
0 |
if ($start - $left >= 1) { }
|
|
|
0 |
0 |
elsif ($start - $left <= 0) { }
|
|
289
|
0 |
0 |
if ($end + $right >= $sizes{'chr' . $chrom}) { }
|
|
299
|
0 |
0 |
if ($end + $right >= $sizes{'chr' . $chrom}) { }
|
|
319
|
0 |
0 |
unless open my $Bed, '<:gzip(autopop)', $bedfile
|
|
326
|
0 |
0 |
unless $line[5]
|
|
336
|
0 |
0 |
if ($line[6])
|
|
360
|
0 |
0 |
unless my $test_fetchChromSizes = can_run('fetchChromSizes')
|
|
366
|
0 |
0 |
if ($success) { }
|
|
371
|
0 |
0 |
unless my $test_fetchChromSizes = can_run('mysql')
|
|
376
|
0 |
0 |
if ($success) { }
|
|
408
|
0 |
0 |
unless defined $dir
|
|
411
|
0 |
0 |
if -d $dir
|
|
412
|
0 |
0 |
unless make_path($dir, {'verbose', 1})
|
|
426
|
0 |
0 |
unless defined $dir
|
|
429
|
0 |
0 |
unless -d $dir
|
|
430
|
0 |
0 |
unless remove_tree($dir, {'verbose', 1})
|