| line |
true |
false |
branch |
|
149
|
1 |
28 |
if ($opts{'concat'}) { } |
|
160
|
0 |
28 |
if ($in_format and $in_format =~ /blast/) { } |
|
162
|
0 |
0 |
$file eq 'STDIN' ? : |
|
173
|
0 |
28 |
$file eq 'STDIN' ? : |
|
178
|
0 |
29 |
$opts{'binary'} ? : |
|
182
|
29 |
0 |
unless $out_format eq "paml" |
|
208
|
0 |
0 |
if ($seq->seq =~ /^-+$/) |
|
213
|
0 |
0 |
unless $ct >= 2 |
|
236
|
0 |
27 |
if $option eq "input" or $option eq "output" or $option eq "noflatname" or $option eq "binary" |
|
238
|
26 |
1 |
if (can_handle($option)) { } |
|
243
|
20 |
1 |
unless $opts{'no-flat'} |
|
244
|
0 |
21 |
if ($out_format eq 'paml') { } |
|
254
|
0 |
0 |
if ($seq->seq =~ /^-+$/) |
|
259
|
0 |
0 |
unless $ct >= 2 |
|
272
|
0 |
0 |
unless length $char == 1 |
|
284
|
0 |
0 |
if ($seq->id eq $refId) { } |
|
291
|
0 |
0 |
unless $refSeq |
|
308
|
0 |
0 |
if $refSeq->alphabet eq "dna" and $seqB->alphabet eq "dna" and not $mA =~ /^[ATCG]$/i && $mB =~ /^[ATCG]$/i |
|
310
|
0 |
0 |
if $mA eq "-" or $mB eq "-" |
|
312
|
0 |
0 |
unless $mA eq $mB |
|
331
|
0 |
0 |
if $match_symbols_full[$i] eq "*" |
|
359
|
0 |
0 |
if $seqA->alphabet eq "dna" and $seqB->alphabet eq "dna" and not $mA =~ /^[ATCG]$/i && $mB =~ /^[ATCG]$/i |
|
360
|
0 |
0 |
unless $mA eq $mB |
|
362
|
0 |
0 |
if $mA eq "-" or $mB eq "-" |
|
364
|
0 |
0 |
unless $mA eq $mB |
|
385
|
0 |
0 |
if ($line =~ /^>(\S+)\s+(\d+)/) { } |
|
432
|
0 |
0 |
if ($nts[$i] eq '-') { } |
|
433
|
0 |
0 |
if ($gap_start) { } |
|
440
|
0 |
0 |
if ($gap_start) { } |
|
448
|
0 |
0 |
if $gap_start |
|
455
|
0 |
0 |
if $gap->{'start'} == 1 |
|
456
|
0 |
0 |
if $gap->{'end'} == $aln->length |
|
459
|
0 |
0 |
unless @three_end_gaps or @five_end_gaps |
|
467
|
0 |
0 |
if ($gap->{'length'} > $longest_three_length) |
|
474
|
0 |
0 |
if ($gap->{'length'} > $longest_five_length) |
|
481
|
0 |
0 |
if (@three_end_gaps) |
|
487
|
0 |
0 |
if (@five_end_gaps) |
|
502
|
0 |
0 |
if ($nts[$i] eq '-') { } |
|
503
|
0 |
0 |
if ($gap_start) { } |
|
510
|
0 |
0 |
if ($gap_start) { } |
|
518
|
0 |
0 |
if $gap_start |
|
534
|
0 |
0 |
$start == 1 || $end == $aln->length ? : |
|
|
0 |
0 |
($end - $start + 1) % 3 ? : |
|
552
|
0 |
0 |
if ($nts[$i] eq '-') { } |
|
553
|
0 |
0 |
if ($gap_start) { } |
|
560
|
0 |
0 |
if ($gap_start) { } |
|
568
|
0 |
0 |
if $gap_start |
|
585
|
0 |
0 |
$start == 1 || $end == $aln->length ? : |
|
|
0 |
0 |
($end - $start + 1) % 3 ? : |
|
590
|
0 |
0 |
unless $Bio::BPWrapper::AlnManipulations::a->{'start'} <=> $Bio::BPWrapper::AlnManipulations::b->{'start'} |
|
675
|
2 |
24 |
if $i == 0 |
|
681
|
26 |
1534 |
if $j % $block_length == 0 |
|
684
|
520 |
1040 |
if ($j + 1) % 3 == 0 |
|
687
|
26 |
1534 |
if ($j + 1 == $aln_length or ($j + 1) % $block_length == 0) |
|
688
|
2 |
24 |
if ($i + 1 == $num_seqs) { } |
|
695
|
1 |
25 |
if ($i + 1 == $num_seqs and $nuc_count == $aln_length) { } |
|
|
1 |
48 |
elsif ($i + 1 == $num_seqs and $nuc_count < $aln_length) { } |
|
788
|
0 |
1 |
if ($opts{'concat'}) { } |
|
816
|
0 |
1 |
if $begin eq "-" |
|
817
|
0 |
1 |
if $end eq "-" |
|
837
|
0 |
0 |
if $_ eq "-" |
|
845
|
0 |
0 |
if $ref->{$key} == 1 |
|
869
|
0 |
0 |
if &_has_gap([values %seen]) |
|
870
|
0 |
0 |
if keys %seen != 2 |
|
871
|
0 |
0 |
if &_has_singleton(\%seen) |
|
878
|
0 |
0 |
unless @inf_sites |
|
885
|
0 |
0 |
$binary ? : |
|
906
|
0 |
0 |
unless $_ eq $refId |
|
909
|
0 |
0 |
unless $seenRef |
|
915
|
0 |
0 |
if &_has_gap([values %seen]) |
|
916
|
0 |
0 |
if keys %seen != 2 |
|
918
|
0 |
0 |
if ($base1 eq $ref_bases->{$refId}{$i}) { } |
|
928
|
0 |
0 |
unless @inf_sites |
|
962
|
2 |
88 |
if ($is_constant < 1) |
|
971
|
26 |
312 |
if $_->{'id'} eq $id |
|
1018
|
0 |
1 |
$opts{'ref-seq'} ? : |
|
1037
|
30 |
90 |
if $refSeq->subseq($i, $i) eq "-" |
|
1070
|
0 |
90 |
unless $pos >= $range{$gene}{'start'} and $pos <= $range{$gene}{'end'} |
|
1084
|
0 |
1 |
if $nseq < 2 |
|
1092
|
87 |
33 |
if ($in_block) { } |
|
1093
|
85 |
2 |
if ($is_constant) { } |
|
1098
|
1 |
84 |
if ($i == $len) |
|
1100
|
1 |
0 |
if $block->{'length'} >= $min_block_size |
|
1104
|
2 |
0 |
if $block->{'length'} >= $min_block_size |
|
1108
|
3 |
30 |
if ($is_constant) |
|
1125
|
13728 |
1144 |
unless $_->{'id'} eq $id |
|
1126
|
39 |
1105 |
if $i == 0 |
|
1127
|
39 |
1105 |
if $i == $#sites |
|
1168
|
1 |
12 |
if ($_->id =~ /$id/) |
|
1170
|
0 |
1 |
if not $nmatch or $nmatch > 1 |
|
1173
|
1 |
0 |
if ($ct_gap) { } |
|
1208
|
0 |
1 |
if $nseq < 2 |
|
1266
|
1 |
0 |
$opts{'resample'} == 0 ? : |
|
1268
|
0 |
1 |
if $sample_size > $num_seqs |
|
1273
|
4 |
3 |
if rand() <= $sample_size / $j |
|
1296
|
0 |
0 |
if $nseq < 2 |
|
1315
|
0 |
0 |
if $_->{'id'} eq $id |
|
1340
|
0 |
1 |
if $nseq < 2 |
|
1367
|
0 |
0 |
if $nseq < 2 |
|
1373
|
0 |
0 |
if $i % 3 |
|
1416
|
1 |
1 |
if ($nuc_count + $block_length >= $aln_length) { } |
|
1433
|
2 |
0 |
if length $start_pos < $last_pos_len |
|
1450
|
1 |
1 |
$need_new ? : |
|
1456
|
60 |
5 |
unless $seqid eq $_ |
|
1460
|
1 |
1 |
if $need_new == 1 |
|
1470
|
30 |
90 |
if ($chars[$i] eq "-") |
|
1493
|
109635 |
37980 |
unless $state eq "-" |
|
1496
|
360 |
2370 |
$state eq '-' ? : |
|
1524
|
34 |
176 |
if @keys > 1 |
|
1536
|
0 |
0 |
if $_ =~ /[\-\?]/ |
|
1541
|
0 |
0 |
if ($_ < 2) |
|
1543
|
0 |
0 |
if @keys > 1 |