| line |
true |
false |
branch |
|
29
|
4 |
0 |
if ($@)
|
|
58
|
0 |
0 |
if ($iThreads)
|
|
152
|
0 |
0 |
unless $seqfile
|
|
160
|
0 |
0 |
unless defined $settings->{'sample'}
|
|
166
|
0 |
0 |
if (ref $seqfile and $seqfile->isa('Bio::SeqIO'))
|
|
173
|
0 |
0 |
if ($@)
|
|
199
|
0 |
0 |
unless -e $seqfile
|
|
228
|
0 |
0 |
if ($self->{'kmercounter'} =~ /(pure)?.*perl/) { }
|
|
|
0 |
0 |
elsif ($self->{'kmercounter'} =~ /jellyfish/) { }
|
|
266
|
0 |
0 |
if ($self->{'kmercounter'} eq 'perl') { }
|
|
|
0 |
0 |
elsif ($self->{'kmercounter'} eq 'jellyfish') { }
|
|
267
|
0 |
0 |
unless ($iThreads)
|
|
279
|
0 |
0 |
if ($self->{'sample'} < 1)
|
|
288
|
0 |
0 |
if ($sample >= rand 1)
|
|
342
|
0 |
0 |
if (length $query != $self->{'kmerlength'})
|
|
347
|
0 |
0 |
if ($self->{'kmercounter'} eq 'perl') { }
|
|
|
0 |
0 |
elsif ($self->{'kmercounter'} eq 'jellyfish') { }
|
|
351
|
0 |
0 |
unless open my $queryFh, "$self->{'jellyfish'} query " . $self->{'jellyfishdb'} . ' |'
|
|
354
|
0 |
0 |
if $?
|
|
381
|
0 |
0 |
if (@{$self->{'_hist'};} > 0)
|
|
385
|
0 |
0 |
if ($self->{'kmercounter'} eq 'jellyfish') { }
|
|
400
|
0 |
0 |
if $?
|
|
404
|
0 |
0 |
unless open my $fh, $self->{'histfile'}
|
|
496
|
0 |
0 |
if ($count < $self->{'gt'})
|
|
528
|
0 |
0 |
if keys %{$$self{'_kmers'};} > 0
|
|
532
|
0 |
0 |
if ($self->{'kmercounter'} eq 'jellyfish')
|
|
537
|
0 |
0 |
unless open my $fh, $self->{'kmerfile'}
|
|
568
|
0 |
0 |
unless ($self->_checkCompatibility($other))
|
|
601
|
0 |
0 |
unless ($self->_checkCompatibility($other))
|
|
608
|
0 |
0 |
if ($kmer2->{$kmer})
|
|
634
|
0 |
0 |
unless ($self->_checkCompatibility($other))
|
|
653
|
0 |
0 |
if ($self->{'kmerlength'} != $other->{'kmerlength'})
|
|
654
|
0 |
0 |
if $self->{'verbose'}
|
|
689
|
0 |
0 |
if ($jfVersion =~ /(jellyfish\s+)?(\d+)?/)
|
|
691
|
0 |
0 |
if ($majorVersion < 2)
|
|
702
|
0 |
0 |
if ($seqfile =~ /\.gz$/i) { }
|
|
703
|
0 |
0 |
unless (-e $zcat)
|
|
706
|
0 |
0 |
if $?
|
|
712
|
0 |
0 |
if $?
|
|
720
|
0 |
0 |
if -s $kmerTsv > 0
|
|
724
|
0 |
0 |
if (-s $kmerTsv < 1)
|
|
727
|
0 |
0 |
if $?
|
|
740
|
0 |
0 |
unless (grep /$ext/, @fastqExt)
|
|
747
|
0 |
0 |
if ($ext =~ /\.gz$/) { }
|
|
751
|
0 |
0 |
if (-e $gzip) { }
|
|
752
|
0 |
0 |
unless open $fh, "$gzip -cd \Q$fastq\E | "
|
|
754
|
0 |
0 |
unless $fh = 'IO::Uncompress::Gunzip'->new($fastq)
|
|
757
|
0 |
0 |
unless open $fh, '<', $fastq
|