| line |
true |
false |
branch |
|
65
|
0 |
0 |
if ref($value) =~ /Fastq/
|
|
66
|
0 |
0 |
unless defined $value
|
|
82
|
0 |
0 |
unless (defined $fasta_file)
|
|
87
|
0 |
0 |
unless (-f $fasta_file)
|
|
92
|
0 |
0 |
unless ($fasta_file =~ /.+\.(fasta|fa|fna|ffn)(\.gz)?$/)
|
|
96
|
0 |
0 |
if @$args
|
|
111
|
0 |
0 |
if ($opts->{'prefix'} =~ m(([/\\])))
|
|
116
|
0 |
0 |
if ($opts->{'jobs'} <= 0)
|
|
121
|
0 |
0 |
if (0 > $opts->{'sequencing-error'} or $opts->{'sequencing-error'} > 1)
|
|
126
|
0 |
0 |
if (not exists $QUALITY_PROFILE{$opts->{'quality-profile'}} and $opts->{'quality-profile'} ne 'poisson')
|
|
132
|
0 |
0 |
if (0 > $opts->{'read-size'})
|
|
139
|
0 |
0 |
if (not $sizes{$opts->{'read-size'}} and $opts->{'quality-profile'} ne 'poisson')
|
|
145
|
0 |
0 |
unless (exists $STRAND_BIAS{$opts->{'strand-bias'}})
|
|
151
|
0 |
0 |
unless (exists $SEQUENCING_TYPE{$opts->{'sequencing-type'}})
|
|
158
|
0 |
0 |
if ($opts->{'sequencing-type'} eq 'paired-end')
|
|
160
|
0 |
0 |
if ($opts->{'fragment-mean'} <= 0)
|
|
165
|
0 |
0 |
if ($opts->{'fragment-stdd'} < 0)
|
|
170
|
0 |
0 |
if ($opts->{'fragment-mean'} - $opts->{'fragment-stdd'} < $opts->{'read-size'})
|
|
179
|
0 |
0 |
if (exists $opts->{'number-of-reads'})
|
|
181
|
0 |
0 |
if ($opts->{'number-of-reads'} <= 0)
|
|
186
|
0 |
0 |
if ($opts->{'number-of-reads'} < 2 and $opts->{'sequencing-type'} eq 'paired-end')
|
|
192
|
0 |
0 |
if ($opts->{'coverage'} <= 0)
|
|
197
|
0 |
0 |
unless (exists $SEQID_WEIGHT{$opts->{'seqid-weight'}})
|
|
203
|
0 |
0 |
if ($opts->{'seqid-weight'} eq 'file')
|
|
204
|
0 |
0 |
unless (defined $opts->{'weight-file'})
|
|
209
|
0 |
0 |
if (not -f $opts->{'weight-file'})
|
|
226
|
0 |
0 |
if exists $opts->{'number-of-reads'}
|
|
231
|
0 |
0 |
if (@$err_list)
|
|
276
|
0 |
0 |
if ($opts->{'sequencing-type'} eq 'paired-end') { }
|