| line |
true |
false |
branch |
|
66
|
0 |
15 |
if ($in_format eq 'edge') { } |
|
69
|
0 |
15 |
$file eq 'STDIN' ? : |
|
75
|
225 |
195 |
if $_->is_Leaf |
|
84
|
0 |
0 |
if ($nd->is_Leaf) |
|
92
|
0 |
0 |
if $decCts >= $cutoff |
|
107
|
0 |
0 |
unless /^(\S+)\s+(\S+)/ |
|
110
|
0 |
0 |
unless $parent{$ch} |
|
129
|
0 |
0 |
if $add_node{$pa} |
|
138
|
0 |
0 |
if $node eq $rootnode |
|
143
|
0 |
0 |
if (@nds) { } |
|
156
|
0 |
0 |
unless $opts{'ref'} |
|
166
|
0 |
0 |
if ($nd->is_Leaf) |
|
175
|
0 |
0 |
if $ref eq $_->id |
|
177
|
0 |
0 |
if ($in_des) { } |
|
197
|
0 |
0 |
unless $opts{'trim-tips'} |
|
216
|
0 |
0 |
if $otu_sets{$_->id} |
|
235
|
0 |
0 |
if $node->is_Leaf |
|
240
|
0 |
0 |
unless $des->is_Leaf |
|
245
|
0 |
0 |
if $dist > $$ref_cut |
|
248
|
0 |
0 |
if ($trim) { } |
|
275
|
0 |
0 |
if $nd->is_Leaf |
|
280
|
0 |
0 |
unless $opts{'cut-tree'} |
|
282
|
0 |
0 |
if $cut >= $least_otu_height |
|
288
|
0 |
0 |
$cutnode->is_Leaf ? : |
|
301
|
0 |
0 |
if $node->{'height'} > $$ref_cut |
|
303
|
0 |
0 |
if ($des->{'height'} > $$ref_cut) |
|
304
|
0 |
0 |
unless $des->is_Leaf |
|
322
|
0 |
0 |
if $nd->is_Leaf |
|
323
|
0 |
0 |
if ($labs{$nd->internal_id}) { } |
|
344
|
0 |
0 |
unless $nd->is_Leaf |
|
346
|
0 |
0 |
if ($labs{$nd->id}) { } |
|
370
|
0 |
0 |
unless $nd->is_Leaf |
|
371
|
0 |
0 |
if $nd->{'xcoord'} >= $longest_leaf_length |
|
384
|
0 |
0 |
$nd->is_Leaf ? : |
|
385
|
0 |
0 |
$dashes ? : |
|
394
|
0 |
0 |
if $current_node eq $rootnode |
|
400
|
0 |
0 |
if $node eq $current_node or $node eq $parent_node |
|
401
|
0 |
0 |
if $current_ycoord < $parent_ycoord and $node->{'ycoord'} < $current_ycoord || $node->{'ycoord'} > $parent_ycoord |
|
402
|
0 |
0 |
if $current_ycoord > $parent_ycoord and $node->{'ycoord'} > $current_ycoord || $node->{'ycoord'} < $parent_ycoord |
|
406
|
0 |
0 |
unless $chars[$parent_xcoord + 1] eq "+" |
|
418
|
0 |
0 |
if $node->is_Leaf |
|
420
|
0 |
0 |
if ($child->is_Leaf) { } |
|
433
|
0 |
0 |
unless defined $child->{'ycoord'} |
|
450
|
0 |
0 |
if defined $parent |
|
462
|
0 |
0 |
if ($first_line) |
|
471
|
0 |
0 |
unless @colnames == @data |
|
473
|
0 |
0 |
$data[$i] ? : |
|
489
|
0 |
0 |
unless &_is_informative($colnames[$i], $i) |
|
492
|
0 |
0 |
if @{$rootnode->get_tag_values($colnames[$i]);} == 2 |
|
503
|
0 |
0 |
if ($node->is_Leaf) { } |
|
509
|
0 |
0 |
if ($child[0]->is_Leaf) { } |
|
511
|
0 |
0 |
if ($child[1]->is_Leaf) { } |
|
520
|
0 |
0 |
if ($child[1]->is_Leaf) { } |
|
537
|
0 |
0 |
if $union{$e}++ |
|
541
|
0 |
0 |
if (@$ref1 == @$ref2) { } |
|
556
|
0 |
0 |
if $nd->is_Leaf |
|
557
|
0 |
0 |
if ($pa = $nd->ancestor) { } |
|
573
|
0 |
0 |
if (keys %seen == 1) |
|
576
|
0 |
0 |
if ($seen{$_} == 1) |
|
589
|
0 |
0 |
if $nd eq $rootnode |
|
593
|
0 |
0 |
if ($state ne $pa_state) |
|
611
|
0 |
0 |
if $st eq $id |
|
622
|
0 |
0 |
if ($nd->is_Leaf) { } |
|
630
|
0 |
0 |
if $nd->is_Leaf or $nd eq $rootnode |
|
632
|
0 |
0 |
unless @dscs == 2 |
|
634
|
0 |
0 |
$dscs[0]->is_Leaf ? : |
|
636
|
0 |
0 |
$dscs[1]->is_Leaf ? : |
|
637
|
0 |
0 |
if ($nd eq $rootnode) { } |
|
655
|
0 |
0 |
if $nd eq $rootnode |
|
658
|
0 |
0 |
if ($nd->is_Leaf) { } |
|
670
|
0 |
0 |
if $nd->is_Leaf |
|
676
|
0 |
0 |
if (@nds) |
|
708
|
0 |
0 |
unless $_->is_Leaf |
|
714
|
0 |
0 |
if ($opts{'swap-otus'}) { } |
|
721
|
0 |
0 |
if $nd eq $ref_otu |
|
735
|
0 |
1 |
if (scalar @dnodes != 2) { } |
|
743
|
0 |
0 |
unless $_->is_Leaf |
|
754
|
0 |
0 |
$pa_i eq $pa_j ? : |
|
768
|
15 |
13 |
if $_->is_Leaf |
|
782
|
0 |
0 |
if ($tag eq 'otu') { } |
|
|
0 |
0 |
elsif ($tag eq 'intid') { } |
|
786
|
0 |
0 |
if ($nd->internal_id == $out_id) |
|
797
|
0 |
0 |
unless $outgroup |
|
804
|
0 |
0 |
if $opts{'clean-br'} |
|
805
|
0 |
0 |
if ($opts{'clean-boot'}) |
|
807
|
0 |
0 |
unless $nd->is_Leaf |
|
823
|
0 |
0 |
if $nd->is_Leaf |
|
836
|
0 |
0 |
unless $to_del{$nd->id} |
|
853
|
0 |
0 |
if scalar @desc <= 2 |
|
873
|
1 |
1 |
if ($opts{'subset'}) { } |
|
897
|
44 |
12 |
unless exists $keep{$_->internal_id} |
|
904
|
2 |
10 |
if $nd == $rootnode |
|
906
|
5 |
5 |
unless scalar @desc == 1 |
|
916
|
1 |
1 |
if (scalar @desc == 1) |
|
925
|
15 |
13 |
if $_->is_Leaf |
|
931
|
1 |
0 |
if (_name2node($opts{'lca'})) { } |
|
937
|
1 |
0 |
if (@lca_nodes > 1) { } |
|
|
0 |
0 |
elsif (@lca_nodes == 1) { } |
|
943
|
1 |
0 |
if (_name2node($opts{'lca'})) { } |
|
945
|
0 |
0 |
if (_name2node($opts{'lca'})) { } |
|
953
|
1 |
27 |
if $_ == $rootnode |
|
954
|
27 |
0 |
defined $_->id ? : |
|
963
|
15 |
13 |
if $_->is_Leaf |
|
1003
|
1 |
9 |
if $_ < "1e-10" |
|
1016
|
1 |
27 |
if $_ == $rootnode |
|
1020
|
15 |
12 |
$_->is_Leaf ? : |
|
1028
|
0 |
1 |
$opts{'random'} == 0 ? : |
|
1030
|
0 |
1 |
if $sample_size > scalar @otus |
|
1035
|
3 |
11 |
if rand() < $sample_size / $_ |
|
1056
|
0 |
1 |
if ($inode_id eq 'all') { } |
|
1061
|
1 |
0 |
if ($nd->is_Leaf) { } |
|
1131
|
0 |
0 |
unless $_->is_Leaf |
|
1133
|
0 |
0 |
if ($dis > $maxL) |
|
1142
|
0 |
0 |
unless $_->is_Leaf or $_ eq $node1 |
|
1144
|
0 |
0 |
if ($dis > $maxL) |
|
1151
|
0 |
0 |
unless $nd |
|
1170
|
0 |
0 |
if $sumL >= $mL / 2 |
|
1171
|
0 |
0 |
if $nd->ancestor eq $rootnode |
|
1186
|
0 |
15 |
if $opts->{'ids-all'} |
|
1187
|
0 |
15 |
if $opts->{'rename-tips'} |
|
1188
|
0 |
15 |
if $opts->{'as-text'} |
|
1189
|
0 |
15 |
if $opts->{'cut-tree'} |
|
1190
|
0 |
15 |
if $opts->{'trim-tips'} |
|
1191
|
0 |
15 |
if $opts->{'cut-sis'} |
|
1192
|
0 |
15 |
if $opts->{'mid-point'} |
|
1193
|
0 |
15 |
if $opts->{'ci'} |
|
1194
|
1 |
14 |
if $opts->{'dist'} |
|
1195
|
0 |
15 |
if $opts->{'del-low-boot'} |
|
1196
|
0 |
15 |
if $opts->{'del-short-br'} |
|
1197
|
1 |
14 |
if $opts->{'length'} |
|
1198
|
1 |
14 |
if $opts->{'otus-num'} |
|
1199
|
1 |
14 |
if defined $opts->{'output'} |
|
1200
|
0 |
15 |
if $opts->{'reroot'} |
|
1201
|
0 |
15 |
if $opts->{'ref'} |
|
1202
|
1 |
14 |
if $opts->{'subset'} |
|
1203
|
1 |
14 |
if $opts->{'otus-all'} |
|
1204
|
1 |
14 |
if $opts->{'lca'} |
|
1205
|
1 |
14 |
if $opts->{'label-nodes'} |
|
1206
|
0 |
15 |
if $opts->{'label-selected-nodes'} |
|
1207
|
1 |
14 |
if $opts->{'dist-all'} |
|
1208
|
1 |
14 |
if $opts->{'ltt'} |
|
1209
|
1 |
14 |
if $opts->{'length-all'} |
|
1210
|
1 |
14 |
if defined $opts->{'random'} |
|
1211
|
1 |
14 |
if $opts->{'depth'} |
|
1212
|
0 |
15 |
if $opts->{'tips-to-root'} |
|
1213
|
0 |
15 |
if $opts->{'rotate-node'} |
|
1215
|
1 |
14 |
if $opts->{'otus-desc'} |
|
1216
|
1 |
14 |
if $opts->{'walk'} |
|
1217
|
0 |
15 |
if $opts->{'walk-edge'} |
|
1218
|
0 |
15 |
if $opts->{'multi2bi'} |
|
1219
|
0 |
15 |
if $opts->{'clean-br'} or $opts->{'clean-boot'} |
|
1220
|
0 |
15 |
if $opts->{'del-otus'} |
|
1221
|
0 |
15 |
if $opts->{'sis-pairs'} |
|
1222
|
0 |
15 |
if $opts->{'swap-otus'} |
|
1223
|
0 |
15 |
if $opts->{'ead'} |
|
1224
|
0 |
15 |
if $opts->{'tree-shape'} |
|
1225
|
4 |
11 |
if $print_tree |
|
1234
|
0 |
0 |
if $nd->is_Leaf |
|
1238
|
0 |
0 |
unless ($nd->id) |
|
1242
|
0 |
0 |
if ($nd->id < $bootcut) |
|
1254
|
0 |
0 |
if $nd->is_Leaf |
|
1258
|
0 |
0 |
if ($nd->branch_length and $nd->branch_length <= $brcut) |
|
1274
|
17 |
0 |
if ($nd) { } |
|
1283
|
0 |
1 |
if $nd->is_Leaf |
|
1284
|
15 |
12 |
if $_->is_Leaf |
|
1301
|
0 |
0 |
if ($_->is_Leaf) { } |
|
1309
|
0 |
0 |
unless (exists $visited{$_}) |
|
1311
|
0 |
0 |
if exists $visited{$_} |
|
1338
|
1 |
27 |
if $_->depth > $height |
|
1348
|
107 |
106 |
unless $$noderef->is_Leaf |
|
1352
|
203 |
21 |
if $_->depth <= $upper |
|
1370
|
15 |
12 |
if ($_->is_Leaf) { } |
|
1372
|
1 |
14 |
if exists $visited{$_} |
|
1379
|
0 |
14 |
if $opts{'walk-edge'} |
|
1380
|
14 |
0 |
if $opts{'walk'} |
|
1384
|
3 |
9 |
if exists $visited{$_} |
|
1389
|
0 |
9 |
if $opts{'walk-edge'} |