| line |
true |
false |
branch |
|
98
|
25 |
0 |
unless (defined $self->sequence_factory) |
|
129
|
0 |
15 |
if $self->{'_readfile'} |
|
131
|
0 |
15 |
unless ($fh) |
|
132
|
0 |
0 |
if (not fileno ARGV or eof ARGV) |
|
133
|
0 |
0 |
unless my $ARGV = shift() |
|
134
|
0 |
0 |
unless open ARGV, $ARGV |
|
139
|
0 |
15 |
unless read $fh, $buffer, 128 |
|
148
|
4 |
11 |
if ($creator->{'header'}{'version'} lt '3.00') { } |
|
183
|
0 |
44 |
if ($creator->{'header'}{'sample_size'} == 1) |
|
196
|
142333 |
282591 |
if ($_ > 30000) |
|
203
|
0 |
44 |
if ($creator->{'header'}{'sample_size'} == 1) |
|
205
|
0 |
0 |
if $_ < 0 |
|
239
|
7 |
8 |
if (@name_comments) |
|
286
|
1733 |
5906 |
if ($currbase eq 'a') { } |
|
|
2691 |
3215 |
elsif ($currbase eq 'c') { } |
|
|
1227 |
1988 |
elsif ($currbase eq 'g') { } |
|
|
1988 |
0 |
elsif ($currbase eq 't') { } |
|
367
|
13 |
2 |
if (@comments_split) |
|
370
|
74 |
26 |
if ($1 and $2) |
|
442
|
828 |
2906 |
if ($currbase eq 'a') { } |
|
|
1238 |
1668 |
elsif ($currbase eq 'c') { } |
|
|
710 |
958 |
elsif ($currbase eq 'g') { } |
|
|
958 |
0 |
elsif ($currbase eq 't') { } |
|
472
|
0 |
4 |
if ($sample_size == 1) { } |
|
542
|
0 |
0 |
if ($transformed) { } |
|
615
|
10 |
0 |
if (ref($swq) =~ /Bio::Seq::SequenceTrace|Bio::Seq::Quality/) { } |
|
616
|
2 |
8 |
if (ref $swq eq 'Bio::Seq::Quality') |
|
629
|
10 |
13 |
if $arg =~ /target/i |
|
633
|
10 |
0 |
unless ($comments{'NAME'}) |
|
635
|
10 |
0 |
unless defined $comments{'CONV'} |
|
637
|
1 |
9 |
if ($writer_fodder->{'comments'}{'version'}) { } |
|
638
|
0 |
1 |
if ($writer_fodder->{'comments'}{'version'} != 2 and $writer_fodder->{'comments'}{'version'} != 3) { } |
|
|
0 |
1 |
elsif ($writer_fodder->{'comments'}{'version'} > 2) { } |
|
676
|
1 |
9 |
if ($writer_fodder->{'header'}{'version'} == 2) { } |
|
694
|
0 |
1 |
if $self->verbose > 0 |
|
695
|
0 |
1 |
unless $self->_print($writer_fodder->{'header'}{'binary'}) |
|
697
|
0 |
1 |
unless $self->_print($writer_fodder->{'traces'}{'binary'}) |
|
699
|
0 |
1 |
unless $self->_print($writer_fodder->{'bases'}{'binary'}) |
|
701
|
0 |
1 |
unless $self->_print($writer_fodder->{'comments'}{'binary'}) |
|
737
|
0 |
9 |
unless $self->_print($writer_fodder->{'header'}{'binary'}) |
|
739
|
0 |
9 |
unless $self->_print($writer_fodder->{'traces'}{'binary'}) |
|
741
|
0 |
9 |
unless $self->_print($writer_fodder->{'peak_indices'}{'binary'}) |
|
743
|
0 |
9 |
unless $self->_print($writer_fodder->{'accuracies'}{'binary'}) |
|
745
|
0 |
9 |
unless $self->_print($writer_fodder->{'bases'}{'binary'}) |
|
747
|
0 |
9 |
unless $self->_print($writer_fodder->{'reserved'}{'binary'}) |
|
749
|
0 |
9 |
unless $self->_print($writer_fodder->{'comments'}{'binary'}) |
|
755
|
10 |
0 |
if $self->_flush_on_write and defined $self->_fh |
|
823
|
0 |
10 |
if (ref $ref eq 'Bio::Seq::Quality') { } |
|
831
|
1 |
9 |
if ($version eq '2') { } |
|
|
9 |
0 |
elsif ($version == 3) { } |
|
843
|
0 |
245300 |
if ($_ > 30000) |
|
848
|
0 |
36 |
if ($sample_size == 1) |
|
850
|
0 |
0 |
if $_ < 0 |
|
861
|
0 |
10 |
if ($sample_size == 1) { } |
|
873
|
0 |
10 |
if ($sample_size == 1) { } |
|
876
|
1 |
9 |
if ($version == 2) { } |
|
956
|
0 |
0 |
if ($version == 2) { } |
|
|
0 |
0 |
elsif ($version == 3) { } |
|
958
|
0 |
0 |
unless defined $as[$curr] |
|
959
|
0 |
0 |
unless defined $cs[$curr] |
|
960
|
0 |
0 |
unless defined $gs[$curr] |
|
961
|
0 |
0 |
unless defined $ts[$curr] |
|
1070
|
36 |
44 |
if ($direction eq 'forward') { } |
|
|
44 |
0 |
elsif ($direction eq 'backward') { } |
|
1071
|
0 |
36 |
if ($SLOW_BUT_CLEAR) { } |
|
1092
|
0 |
44 |
if ($SLOW_BUT_CLEAR) { } |
|
1158
|
81 |
19 |
if ($start_position) |
|
1162
|
81 |
19 |
if ($start_position) { } |
|
1171
|
0 |
100 |
unless (length $buffer == $length) |
|
1177
|
0 |
0 |
if (length $buffer != $length) |
|
1198
|
0 |
0 |
unless ($rhash =~ /HASH/) |