| 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 $seqfile |
|
229
|
0 |
0 |
if ($self->{'kmercounter'} =~ /(pure)?.*perl/) { } |
|
|
0 |
0 |
elsif ($self->{'kmercounter'} =~ /jellyfish/) { } |
|
275
|
0 |
0 |
if ($self->{'_ntcount'}) |
|
284
|
0 |
0 |
if ($length < 1) |
|
315
|
0 |
0 |
if ($self->{'kmercounter'} eq 'perl') { } |
|
|
0 |
0 |
elsif ($self->{'kmercounter'} eq 'jellyfish') { } |
|
316
|
0 |
0 |
unless ($iThreads) |
|
328
|
0 |
0 |
if ($self->{'sample'} < 1) |
|
337
|
0 |
0 |
if ($sample >= rand 1) |
|
391
|
0 |
0 |
if (length $query != $self->{'kmerlength'}) |
|
396
|
0 |
0 |
if ($self->{'kmercounter'} eq 'perl') { } |
|
|
0 |
0 |
elsif ($self->{'kmercounter'} eq 'jellyfish') { } |
|
400
|
0 |
0 |
unless open my $queryFh, "$self->{'jellyfish'} query " . $self->{'jellyfishdb'} . ' |' |
|
403
|
0 |
0 |
if $? |
|
430
|
0 |
0 |
if (@{$self->{'_hist'};} > 0) |
|
434
|
0 |
0 |
if ($self->{'kmercounter'} eq 'jellyfish') { } |
|
449
|
0 |
0 |
if $? |
|
453
|
0 |
0 |
unless open my $fh, $self->{'histfile'} |
|
552
|
0 |
0 |
if ($count < $self->{'gt'}) |
|
584
|
0 |
0 |
if keys %{$$self{'_kmers'};} > 0 |
|
588
|
0 |
0 |
if ($self->{'kmercounter'} eq 'jellyfish') |
|
593
|
0 |
0 |
unless open my $fh, $self->{'kmerfile'} |
|
624
|
0 |
0 |
unless ($self->_checkCompatibility($other)) |
|
657
|
0 |
0 |
unless ($self->_checkCompatibility($other)) |
|
664
|
0 |
0 |
if ($kmer2->{$kmer}) |
|
690
|
0 |
0 |
unless ($self->_checkCompatibility($other)) |
|
709
|
0 |
0 |
if ($self->{'kmerlength'} != $other->{'kmerlength'}) |
|
710
|
0 |
0 |
if $self->{'verbose'} |
|
745
|
0 |
0 |
if ($jfVersion =~ /(jellyfish\s+)?(\d+)?/) |
|
747
|
0 |
0 |
if ($majorVersion < 2) |
|
758
|
0 |
0 |
if ($seqfile =~ /\.gz$/i) { } |
|
759
|
0 |
0 |
unless (-e $zcat) |
|
762
|
0 |
0 |
if $? |
|
768
|
0 |
0 |
if $? |
|
776
|
0 |
0 |
if -s $kmerTsv > 0 |
|
780
|
0 |
0 |
if (-s $kmerTsv < 1) |
|
783
|
0 |
0 |
if $? |
|
796
|
0 |
0 |
unless (grep /$ext/, @fastqExt) |
|
803
|
0 |
0 |
if ($ext =~ /\.gz$/) { } |
|
807
|
0 |
0 |
if (-e $gzip) { } |
|
808
|
0 |
0 |
unless open $fh, "$gzip -cd \Q$fastq\E | " |
|
810
|
0 |
0 |
unless $fh = 'IO::Uncompress::Gunzip'->new($fastq) |
|
813
|
0 |
0 |
unless open $fh, '<', $fastq |