Branch Coverage

lib/Sanger/CGP/TraFiC/Filter.pm
Criterion Covered Total %
branch 3 82 3.6


line true false branch
60 1 2 unless defined which('sort')
76 0 1 unless -e $root_dir
84 0 0 unless -e $clusters and -f $clusters
100 0 0 if ($$cluster_set{'cluster_count'} > 0) { }
110 0 0 if ($$cluster_set{'cluster_count'} > 0 and defined $$self{'germline'})
115 0 0 if ($$cluster_set{'cluster_count'} > 0 and defined $$self{'trans_elements'})
172 0 0 unless exists $$filter{$family}
176 0 0 unless exists $$filter{$family}{$chr}
181 0 0 if ($is_te) { }
193 0 0 if ($remaining_set_clusters == 0)
196 0 0 if scalar @remaining_keys == 0
200 0 0 if $$clusters{'cluster_count'} == 0
202 0 0 if $$clusters{'cluster_count'} < 0
223 0 0 if $filter_i == $filter_tot
230 0 0 if ($$tes[$filter_i][$POS_R_POS] < $q_l_pos)
235 0 0 if ($$tes[$filter_i][$POS_L_POS] > $q_r_pos)
246 0 0 if scalar @l_queries > 0
263 0 0 if $filter_i == $filter_tot
270 0 0 if ($$filters[$filter_i][$POS_R_POS] + $double_read_len < $q_l_pos)
275 0 0 if ($$filters[$filter_i][$POS_L_POS] - $double_read_len > $q_r_pos)
286 0 0 if scalar @l_queries > 0
293 0 0 if (defined $filter)
294 0 0 if (ref $filter eq 'ARRAY') { }
296 0 0 unless -e $_ and -f $_
301 0 0 unless -e $filter and -f $filter
315 0 0 unless ($$self{'assume_sorted'})
322 0 0 unless system($sort_command) == 0
330 0 0 if $line =~ /^#/
334 0 0 if (defined $limit)
336 0 0 if (defined $divergence) { }
337 0 0 unless $limit > $score
341 0 0 if scalar @detail > 10
342 0 0 if $limit > $score
346 0 0 if (defined $query_clusters)
347 0 0 unless exists $$query_clusters{$family} and exists $$query_clusters{$family}{$chr}
363 0 0 if defined $min_reads
369 0 0 if defined $min_reads
375 0 0 if defined $divergence
381 0 0 if defined $readlength
388 0 0 unless -e $file and -f $file
396 0 0 unless -e $file and -f $file