| line |
true |
false |
branch |
|
240
|
0 |
1 |
unless (open my $FILE, '<', $self->{'filename'}) |
|
245
|
114 |
7547 |
if /^AF/ |
|
250
|
581 |
1 |
unless $f =~ /\.singlets$/ |
|
253
|
0 |
1 |
unless (open my $S_FILE, '<', $singlet_file) |
|
257
|
65 |
1226 |
if /^>/ |
|
422
|
0 |
0 |
unless ($contig) |
|
451
|
0 |
0 |
unless $self->{'contigs'}{$currkey}{'name'} |
|
452
|
0 |
0 |
if ($self->{'contigs'}{$currkey}{'name'} eq "$name") |
|
457
|
0 |
0 |
if ($count == 1) |
|
481
|
0 |
0 |
if ($self->{'contigs'}{$currkey}{'name'} and $self->{'contigs'}{$currkey}{'name'} eq "$name") |
|
522
|
0 |
0 |
if (not $self->{'contigs'}{$name}) { } |
|
555
|
488 |
7173 |
if (not $line) { } |
|
|
910 |
6263 |
elsif ($in_contig) { } |
|
|
910 |
5353 |
elsif ($in_quality) { } |
|
|
53 |
5300 |
elsif ($line =~ /^BQ/) { } |
|
|
53 |
5247 |
elsif ($line =~ /^CO/) { } |
|
|
0 |
5247 |
elsif ($line =~ /^BSDEPRECATED/) { } |
|
|
114 |
5133 |
elsif ($line =~ /^AF/) { } |
|
563
|
910 |
0 |
if ($in_contig == 1) |
|
569
|
0 |
910 |
if (not $line) { } |
|
581
|
857 |
53 |
if ($self->{'contigs'}{$contig_number}{'quality'} and not $self->{'contigs'}{$contig_number}{'quality'} =~ /\ $/) |
|
605
|
0 |
53 |
if ($2 eq 'C') |
|
631
|
57 |
57 |
if (not $top) { } |
|
633
|
0 |
57 |
if ($self->{'contigs'}{$contig_number}{'contig_direction'} eq 'C') { } |
|
658
|
0 |
57 |
if ($self->{'contigs'}{$contig_number}{'contig_direction'} eq 'C') { } |
|
735
|
0 |
0 |
if ($ignore_case eq 'yes') |
|
767
|
0 |
0 |
unless ($self->{'doublets_set'}) |
|
773
|
0 |
0 |
if ($self->{'contigs'}{$_}{'class'} eq 'singlet') |
|
782
|
0 |
0 |
if (not $self->{'contigs'}{$_}{'quality'}) { } |
|
825
|
0 |
0 |
if ($self->{'contigs'}{$_}{'class'} eq 'doublet') |
|
887
|
0 |
0 |
if ($dash_present eq 'yes') { } |
|
926
|
118 |
0 |
if ($self->{'contigs'}{$key_contig}{'member_array'}) |
|
932
|
46 |
72 |
if (@{$self->{'contigs'}{$key_contig}{'member_array'};} == 2) { } |
|
|
68 |
4 |
elsif (@{$self->{'contigs'}{$key_contig}{'member_array'};} == 1) { } |
|
|
4 |
0 |
elsif (@{$self->{'contigs'}{$key_contig}{'member_array'};} >= 3) { } |
|
936
|
45 |
1 |
if defined $name |
|
937
|
45 |
1 |
if ($name) { } |
|
955
|
3 |
65 |
unless ($self->{'contigs'}{$key_contig}{'class'}) |
|
990
|
0 |
1 |
if $^O =~ /mswin/i |
|
997
|
0 |
1 |
unless (-f $singletsfile) |
|
1007
|
65 |
1226 |
if (/\>/) { } |
|
1008
|
64 |
1 |
if ($name and $sequence) |
|
1020
|
0 |
65 |
unless ($name) |
|
1027
|
1 |
0 |
if ($name and $sequence) |
|
1056
|
0 |
3 |
unless ($self->{'singlets_set'}) |
|
1067
|
53 |
301 |
if (not $self->{'contigs'}{$key}{'class'}) { } |
|
|
195 |
106 |
elsif ($self->{'contigs'}{$key}{'class'} eq 'singlet') { } |
|
1094
|
0 |
0 |
if ($self->{'contigs'} eq "$name" or $self->{'contigs'}{'name'} eq "$name") |
|
1099
|
0 |
0 |
if ($return) { } |
|
1119
|
0 |
0 |
if $^O =~ /mswin/i |
|
1123
|
0 |
0 |
if (-f $singletsfile) { } |
|
1135
|
0 |
0 |
if ($line =~ /^\>/) { } |
|
1141
|
0 |
0 |
if ($self->{'contigs'}{$identity}) |
|
1171
|
0 |
0 |
if $^O =~ /mswin/i |
|
1175
|
0 |
0 |
if (-f $singletsfile) { } |
|
1187
|
0 |
0 |
if ($line =~ /^\>/) { } |
|
1193
|
0 |
0 |
if ($self->{'contigs'}{$identity}) |
|
1218
|
354 |
0 |
if ($self->{'contigs'}{$key}{'class'}) |
|
1219
|
12 |
342 |
if ($self->{'contigs'}{$key}{'class'} eq 'multiplet') |
|
1244
|
0 |
0 |
if ($key =~ /^singlet/) { } |
|
|
0 |
0 |
elsif ($self->{'contigs'}{$key}{'member_array'}) { } |
|
1294
|
2 |
0 |
if ($multiplet_count) |
|
1300
|
14 |
0 |
unless (${$_;}) |
|
1304
|
0 |
2 |
unless ($multiplet_count) |
|
1305
|
1 |
1 |
if ($total_only) |
|
1368
|
354 |
0 |
if ($self->{'contigs'}{$key}{'class'}) { } |
|
1374
|
354 |
0 |
if ($self->{'contigs'}{$key}{'member_array'}) |
|
1378
|
9 |
195 |
if ($num_array_elem == 1 and $self->{'contigs'}{$key}{'class'} and $self->{'contigs'}{$key}{'class'} eq 'singleton') |
|
1401
|
354 |
0 |
if ($self->{'contigs'}{$key}{'member_array'}) |
|
1402
|
3 |
351 |
if (@{$self->{'contigs'}{$key}{'member_array'};} == 2 and $self->{'contigs'}{$key}{'class'} eq 'pair') |
|
1452
|
92 |
0 |
if ($name) |
|
1455
|
92 |
0 |
if ($suffix) |
|
1459
|
92 |
0 |
if ($suffix) |
|
1460
|
92 |
0 |
if ($suffix =~ /^$forward_designator/ or $suffix =~ /^$reverse_designator/) { } |
|
1472
|
91 |
1 |
if $name_nodir[0] eq $name_nodir[$counter] |
|
1475
|
45 |
1 |
if ($mismatch == 0) { } |
|
1497
|
0 |
3 |
unless ($self->{'doublets_set'}) |
|
1503
|
135 |
219 |
if ($self->{'contigs'}{$_}{'name'} and $self->{'contigs'}{$_}{'class'} eq 'doublet') |
|
1555
|
0 |
0 |
if ($self->{'contigs'}{$_}{'quality'}) { } |
|
1565
|
0 |
0 |
if ($self->{'contigs'}{$_}{'quality'}) { } |
|
1574
|
0 |
0 |
if (not $self->get_name($pair)) { } |
|
1585
|
0 |
0 |
if ($self->{'contigs'}{$contig_number}{'quality'}) { } |
|
1624
|
0 |
0 |
if ($self->{'contigs'}{$current_contig}{'class'} eq 'doublet') |
|
1628
|
0 |
0 |
if ($self->{'contigs'}{$current_contig}{'top_complement'} eq 'C') |
|
1632
|
0 |
0 |
if ($self->{'contigs'}{$current_contig}{'bottom_complement'} eq 'C') |
|
1670
|
0 |
0 |
if (/^BEGIN_DNA/) |
|
1671
|
0 |
0 |
if (/^END_DNA/) |
|
1672
|
0 |
0 |
unless ($in_dna) |
|
1713
|
0 |
0 |
unless (@$r_source) |
|
1717
|
0 |
0 |
unless s/c/g/ or s/g/c/ or s/a/t/ |
|
1747
|
0 |
0 |
if ($self->{'contigs'}{$current_contig}{'class'} eq 'doublet') |
|
1760
|
0 |
0 |
if ($qualities[$count] == 0) |
|
1767
|
0 |
0 |
if (not $bottom_quality_here or 1 - $self->{'contigs'}{$current_contig}{'bottom_start'} + $count < 0) |
|
1770
|
0 |
0 |
unless ($top_quality_here) |
|
1774
|
0 |
0 |
if ($count < $number_leading_xs) { } |
|
1803
|
0 |
0 |
if ($bottom_quality_here eq 'not found') { } |
|
|
0 |
0 |
elsif ($top_quality_here eq 'not found') { } |
|
1831
|
0 |
0 |
if ($bottom_quality > $top_quality) { } |
|
1839
|
0 |
0 |
if (not $quality) { } |
|
1850
|
0 |
0 |
unless (not @qualities) |