| line |
true |
false |
branch |
|
37
|
0 |
0 |
unless -e $bed12
|
|
39
|
0 |
0 |
unless -d $dest
|
|
42
|
0 |
0 |
unless open BED12IN, "< $bed12"
|
|
49
|
0 |
0 |
unless (scalar @blockSize == scalar @blockStart)
|
|
56
|
0 |
0 |
if ($blockCount > 1)
|
|
58
|
0 |
0 |
unless open BED6OUT, "> $bed6_fn"
|
|
64
|
0 |
0 |
if ($can)
|
|
97
|
0 |
0 |
unless -e $bed_in
|
|
99
|
0 |
0 |
unless -d $dest
|
|
102
|
0 |
0 |
unless open INBED, "< $bed_in"
|
|
108
|
0 |
0 |
if ($info =~ /^splits\:(\d+)\:(\d+)\:(\d+):(\w):(\w)/) { }
|
|
112
|
0 |
0 |
unless $proper eq 'N'
|
|
113
|
0 |
0 |
unless $passed =~ /[PFM]$/
|
|
114
|
0 |
0 |
if $reads < $mcov
|
|
121
|
0 |
0 |
if ($can)
|
|
147
|
0 |
0 |
unless -e $bed_in
|
|
149
|
0 |
0 |
unless -d $dest
|
|
157
|
0 |
0 |
unless open INBED, "< $bed_in"
|
|
162
|
0 |
0 |
if ($info =~ /^splits\:(\d+)\:(\d+)\:(\d+):(\w):(\w)/) { }
|
|
166
|
0 |
0 |
if ($circ == 1) { }
|
|
167
|
0 |
0 |
unless $proper =~ /[C]$/
|
|
170
|
0 |
0 |
unless $proper =~ /[N]$/
|
|
172
|
0 |
0 |
unless $passed =~ /[PM]$/
|
|
173
|
0 |
0 |
if $reads < $mcov
|
|
208
|
0 |
0 |
unless my $bedtools = can_run('bedtools')
|
|
209
|
0 |
0 |
unless my $sortBed = can_run('sortBed')
|
|
212
|
0 |
0 |
unless -d $p_annot
|
|
214
|
0 |
0 |
unless -d $p_mapped
|
|
216
|
0 |
0 |
unless -d $dest
|
|
220
|
0 |
0 |
unless opendir $dha, $p_annot
|
|
225
|
0 |
0 |
unless opendir $dhm, $p_mapped
|
|
231
|
0 |
0 |
unless $file =~ /(chr\d+)\_(\d+)-(\d+)/
|
|
237
|
0 |
0 |
if /^(chr\d+)\_(\d+)-(\d+)/ and $2 <= $s5 and $3 >= $s3
|
|
248
|
0 |
0 |
if ($_ =~ /1$/)
|
|
252
|
0 |
0 |
if ($processed % 1000 == 0)
|
|
260
|
0 |
0 |
if (length $prefix > 0)
|
|
270
|
0 |
0 |
if ($file =~ /^(chr\d+\_\d+-\d+)/) { }
|
|
273
|
0 |
0 |
unless open SJ, "< $fn"
|
|
285
|
0 |
0 |
if (exists $asj{$pattern}) { }
|
|
303
|
0 |
0 |
unless ($success)
|
|
314
|
0 |
0 |
unless ($success)
|
|
360
|
0 |
0 |
if ($pattern =~ /^GT|AG$/) { }
|
|
|
0 |
0 |
elsif ($pattern =~ /^CT|AC$/) { }
|
|
|
0 |
0 |
elsif ($pattern =~ /^GC|AG$/) { }
|
|
|
0 |
0 |
elsif ($pattern =~ /^CT|GC$/) { }
|
|
|
0 |
0 |
elsif ($pattern =~ /^AT|AC$/) { }
|
|
|
0 |
0 |
elsif ($pattern =~ /^GT|AT$/) { }
|