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
|