line |
true |
false |
branch |
59
|
0 |
0 |
if exists $$options{'index'} and $index != $$options{'index'}
|
62
|
0 |
0 |
if PCAP::Threaded::success_exists('File::Spec'->catdir($tmp, 'progress'), $index)
|
68
|
0 |
0 |
if $iter++ != $index
|
75
|
0 |
0 |
unless -e $output
|
80
|
0 |
0 |
if (exists $$options{'badloci'})
|
96
|
0 |
0 |
if exists $$options{'index'} and $index != $$options{'index'}
|
99
|
0 |
0 |
if PCAP::Threaded::success_exists('File::Spec'->catdir($tmp, 'progress'), $index)
|
104
|
0 |
0 |
if $iter++ != $index
|
127
|
0 |
0 |
if exists $$options{'index'} and $index != $$options{'index'}
|
130
|
0 |
0 |
if PCAP::Threaded::success_exists('File::Spec'->catdir($tmp, 'progress'), $index)
|
135
|
0 |
0 |
if $iter++ != $index
|
143
|
0 |
0 |
unless -e $outdir
|
160
|
0 |
0 |
if exists $$options{'index'} and $index != $$options{'index'}
|
162
|
0 |
0 |
if PCAP::Threaded::success_exists('File::Spec'->catdir($tmp, 'progress'), $index)
|
169
|
0 |
0 |
if (-e $rm_outdir)
|
180
|
0 |
0 |
if ($file_sample =~ /^${n_name}[.][[:digit:]]+$/) { }
|
|
0 |
0 |
elsif ($file_sample =~ /^${t_name}[.][[:digit:]]+$/) { }
|
191
|
0 |
0 |
if (defined $$options{'rm'}) { }
|
197
|
0 |
0 |
unless defined $repeatmasker
|
221
|
0 |
0 |
if exists $$options{'index'} and $index != $$options{'index'}
|
223
|
0 |
0 |
if PCAP::Threaded::success_exists('File::Spec'->catdir($tmp, 'progress'), $index)
|
226
|
0 |
0 |
if ($index == 1) { }
|
|
0 |
0 |
elsif ($index == 2) { }
|
234
|
0 |
0 |
if (-e $cluster_outdir)
|
246
|
0 |
0 |
if $sample eq $$options{'tumour_name'}
|
257
|
0 |
0 |
if PCAP::Threaded::success_exists('File::Spec'->catdir($tmp, 'progress'), 0)
|
263
|
0 |
0 |
if (exists $$options{'germline'}) { }
|
280
|
0 |
0 |
if (exists $$options{'known'})
|
289
|
0 |
0 |
unless (exists $$options{'germline'})
|
316
|
0 |
0 |
unless -e $path
|
331
|
0 |
0 |
if (-e $indir)
|
332
|
0 |
0 |
unless &opendir(my $dh, $indir)
|
334
|
0 |
0 |
if $thing =~ /^[.]/
|
335
|
0 |
0 |
if $thing =~ /.*[.][[:digit:]]+$/
|