Branch Coverage

lib/Sanger/CGP/TraFiC/Implement.pm
Criterion Covered Total %
branch 0 68 0.0


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 $thing =~ /.*[.][[:digit:]]+$/