| line |
true |
false |
branch |
|
188
|
3 |
0 |
if ($@) { } |
|
230
|
4 |
3 |
if (ref($ingroup) =~ /ARRAY/i) { } |
|
|
3 |
0 |
elsif (ref $ingroup and $ingroup->isa('Bio::PopGen::PopulationI')) { } |
|
243
|
0 |
7 |
if ($seg_sites <= 0) |
|
248
|
0 |
7 |
if (not defined $outgroup) { } |
|
|
4 |
3 |
elsif (ref $outgroup) { } |
|
253
|
0 |
4 |
unless defined $ancestral |
|
280
|
0 |
8 |
if ($n <= 3) |
|
327
|
2 |
1 |
if (ref($individuals) =~ /ARRAY/i) { } |
|
|
1 |
0 |
elsif (ref $individuals and $individuals->isa('Bio::PopGen::PopulationI')) { } |
|
416
|
2 |
3 |
if (ref($ingroup) =~ /ARRAY/i) { } |
|
|
3 |
0 |
elsif (ref $ingroup and $ingroup->isa('Bio::PopGen::PopulationI')) { } |
|
431
|
0 |
5 |
if (not defined $outgroup) { } |
|
|
2 |
3 |
elsif (ref $outgroup) { } |
|
511
|
2 |
1 |
if (ref($individuals) =~ /ARRAY/i) { } |
|
|
1 |
0 |
elsif (ref $individuals and $individuals->isa('Bio::PopGen::PopulationI')) { } |
|
553
|
0 |
4 |
if ($n <= 1) |
|
557
|
0 |
4 |
if ($n == 2) |
|
608
|
2 |
4 |
if (ref($individuals) =~ /ARRAY/i) { } |
|
|
4 |
0 |
elsif (ref $individuals and $individuals->isa('Bio::PopGen::PopulationI')) { } |
|
664
|
0 |
6 |
if $denom == 0 |
|
695
|
9 |
12 |
if (ref($individuals) =~ /ARRAY/i) { } |
|
|
12 |
0 |
elsif (ref $individuals and $individuals->isa('Bio::PopGen::PopulationI')) { } |
|
702
|
0 |
45 |
unless ($ind->isa('Bio::PopGen::IndividualI')) |
|
745
|
568 |
0 |
if ($sampsize > 1) |
|
754
|
2 |
19 |
if ($numsites) { } |
|
789
|
2 |
5 |
if (ref($n) =~ /ARRAY/i) { } |
|
|
4 |
2 |
elsif (ref $n and $n->isa('Bio::PopGen::PopulationI')) { } |
|
810
|
2 |
5 |
if ($totalsites) |
|
813
|
0 |
7 |
if ($a1 == 0) |
|
836
|
5 |
2 |
if (ref($individuals) =~ /ARRAY/) { } |
|
|
2 |
0 |
elsif (ref $individuals and $individuals->isa('Bio::PopGen::PopulationI')) { } |
|
842
|
0 |
2 |
unless (@inds) |
|
856
|
0 |
35 |
unless ($n->isa('Bio::PopGen::IndividualI')) |
|
870
|
128 |
508 |
if $allelect == 1 |
|
902
|
15 |
16 |
if ($type =~ /ARRAY/i) { } |
|
|
16 |
0 |
elsif ($type and $individuals->isa('Bio::PopGen::PopulationI')) { } |
|
905
|
0 |
75 |
unless ($n->isa('Bio::PopGen::IndividualI')) |
|
919
|
636 |
9 |
if keys %$site > 1 |
|
924
|
145 |
18 |
if scalar @alleles > 1 |
|
952
|
0 |
0 |
unless ($freq2) |
|
953
|
0 |
0 |
if ($freq1 > 1 or $freq2 > 1) |
|
986
|
0 |
10 |
unless $otype |
|
991
|
4 |
6 |
if (ref($ingroup) =~ /ARRAY/i) { } |
|
|
6 |
0 |
elsif (ref $ingroup and $ingroup->isa('Bio::PopGen::PopulationI')) { } |
|
992
|
0 |
4 |
unless (ref $ingroup->[0] and $ingroup->[0]->isa('Bio::PopGen::IndividualI')) |
|
1023
|
5 |
5 |
if ($otype =~ /ARRAY/i) { } |
|
|
5 |
0 |
elsif ($otype->isa('Bio::PopGen::PopulationI')) { } |
|
1024
|
0 |
5 |
unless (ref $outgroup->[0] and $outgroup->[0]->isa('Bio::PopGen::IndividualI')) |
|
1070
|
10 |
40 |
if @outalleles > 1 or @in_alleles == 1 |
|
1072
|
40 |
40 |
unless (exists $outdata{$marker}{$allele}) |
|
1073
|
10 |
30 |
if ($indata{$marker}{$allele} == 1) { } |
|
1106
|
0 |
2 |
if (ref($pop) =~ /ARRAY/i) { } |
|
|
0 |
2 |
elsif (not ref $pop && $pop->isa('Bio::PopGen::PopulationI')) { } |
|
1107
|
0 |
0 |
if (ref $pop->[0] and $pop->[0]->isa('Bio::PopGen::IndividualI')) { } |
|
1130
|
0 |
76 |
unless (defined $genotype) |
|
1135
|
3 |
73 |
if scalar @alleles != 2 |
|
1146
|
0 |
5 |
if ($allele_count != 2) |
|
1148
|
0 |
0 |
if $allele_count > 2 |
|
1154
|
0 |
5 |
if (length $alleles[0] != 1 or length $alleles[1] != 1) |
|
1195
|
1 |
52 |
unless scalar @alleles1 == 2 |
|
1203
|
2 |
50 |
unless scalar @alleles2 == 2 |
|
1289
|
0 |
4 |
if ($@) |
|
1327
|
6 |
0 |
if (ref($outgroup) =~ /ARRAY/i) { } |
|
|
0 |
0 |
elsif (UNIVERSAL::isa($outgroup, 'Bio::PopGen::PopulationI')) { } |
|
1335
|
2 |
4 |
if ($polarized) { } |
|
|
0 |
4 |
elsif ($outgroup_count > 1) { } |
|
|
0 |
4 |
elsif ($outgroup_count == 0) { } |
|
1336
|
0 |
2 |
if ($outgroup_count < 2) |
|
1349
|
12 |
0 |
if (ref($p) =~ /ARRAY/i) { } |
|
1356
|
0 |
35 |
if ($unique{$i->unique_id}++) |
|
1365
|
0 |
6 |
if ($marker_names[0] =~ /^(Site|Codon)/) |
|
1396
|
0 |
14126 |
if (@alleles > 2) { } |
|
1403
|
0 |
8971 |
if $AA eq 'X' or $AA eq '*' or $allele =~ /N/i |
|
1406
|
3244 |
5727 |
if ($t eq 'outgroup') |
|
1415
|
810 |
1626 |
if $total and $total < 2 |
|
1418
|
1348 |
278 |
if (keys %{$codonvals{'all'};} <= 1) { } |
|
1423
|
0 |
278 |
unless ($outcodon) |
|
1429
|
0 |
188 |
if ($polarized and $outcodon ne $outcodon2 or $out_AA eq 'X' or $out_AA eq '*') |
|
1434
|
0 |
90 |
if ($verbose > 0) |
|
1453
|
0 |
188 |
if ($verbose > 0) |
|
1464
|
99 |
89 |
if ($diff_from_out) { } |
|
1465
|
92 |
7 |
if (scalar @ingroup_codons == 1) { } |
|
1467
|
0 |
92 |
if ($outcodon =~ /^$gapchar/) { } |
|
|
0 |
92 |
elsif ($ingroup_codons[0] =~ /$gapchar/) { } |
|
1477
|
0 |
92 |
if ($verbose > 0) |
|
1490
|
0 |
14 |
if $c =~ /$gapchar/ or $outcodon =~ /$gapchar/ |
|
1493
|
10 |
4 |
if ($path->[0] < $Ndiff or $tNdiff == $Ndiff and $tSdiff <= $Sdiff) |
|
1501
|
0 |
7 |
if (@ingroup_codons > 2) { } |
|
1509
|
0 |
7 |
if ($verbose > 0) |
|
1525
|
0 |
92 |
unless (defined $path) |
|
1529
|
92 |
0 |
if ($path->[0] < $Ndiff or $tNdiff == $Ndiff and $tSdiff <= $Sdiff) |
|
1536
|
3 |
86 |
if (@unique_codons == 2) |
|
1538
|
0 |
3 |
unless (defined $path) |
|
1546
|
0 |
89 |
if ($verbose > 0) |
|
1584
|
0 |
0 |
if ($has_twotailed) { } |