Branch Coverage

lib/App/SimulateReads/Command/Digest.pm
Criterion Covered Total %
branch 0 58 0.0


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') { }