| line |
true |
false |
branch |
|
68
|
0 |
0 |
if ref($value) =~ /Seq/u
|
|
69
|
0 |
0 |
if $key eq 'argv'
|
|
70
|
0 |
0 |
unless defined $value
|
|
74
|
0 |
0 |
if (ref $value eq 'ARRAY')
|
|
102
|
0 |
0 |
unless (defined $fasta_file)
|
|
107
|
0 |
0 |
unless (-f $fasta_file)
|
|
112
|
0 |
0 |
unless ($fasta_file =~ /.+\.(fasta|fa|fna|ffn)(\.gz)?$/u)
|
|
116
|
0 |
0 |
if @$args
|
|
136
|
0 |
0 |
if ($opts->{'prefix'} =~ m(([/\\]))u)
|
|
141
|
0 |
0 |
if ($opts->{'jobs'} <= 0)
|
|
148
|
0 |
0 |
if ($opts->{'quality-profile'} eq 'poisson') { }
|
|
149
|
0 |
0 |
if (0 >= $opts->{'read-mean'})
|
|
153
|
0 |
0 |
if (0 > $opts->{'read-stdd'})
|
|
158
|
0 |
0 |
if (0 > $opts->{'sequencing-error'} or $opts->{'sequencing-error'} > 1)
|
|
162
|
0 |
0 |
if (%QUALITY_PROFILE and exists $QUALITY_PROFILE{$opts->{'quality-profile'}}) { }
|
|
170
|
0 |
0 |
if $entry->{'type'} eq 'single-molecule'
|
|
178
|
0 |
0 |
if (exists $opts->{'genomic-variation'})
|
|
180
|
0 |
0 |
unless (%STRUCTURAL_VARIATION and exists $STRUCTURAL_VARIATION{$sv})
|
|
188
|
0 |
0 |
if (exists $opts->{'genomic-variation-regex'})
|
|
193
|
0 |
0 |
if ($sv =~ /$pattern/u)
|
|
199
|
0 |
0 |
if ($fail)
|
|
207
|
0 |
0 |
unless (exists $STRAND_BIAS{$opts->{'strand-bias'}})
|
|
213
|
0 |
0 |
unless (exists $SEQUENCING_TYPE{$opts->{'sequencing-type'}})
|
|
220
|
0 |
0 |
if ($opts->{'sequencing-type'} eq 'paired-end')
|
|
222
|
0 |
0 |
if ($opts->{'fragment-mean'} <= 0)
|
|
227
|
0 |
0 |
if ($opts->{'fragment-stdd'} < 0)
|
|
232
|
0 |
0 |
if ($opts->{'fragment-mean'} - $opts->{'fragment-stdd'} < $opts->{'read-mean'} + $opts->{'read-stdd'})
|
|
239
|
0 |
0 |
unless (exists $COUNT_LOOPS_BY{$default_opt{'count-loops-by'}})
|
|
245
|
0 |
0 |
if ($default_opt{'count-loops-by'} eq 'coverage')
|
|
246
|
0 |
0 |
unless (defined $opts->{'coverage'})
|
|
251
|
0 |
0 |
if (defined $opts->{'coverage'} and $opts->{'coverage'} <= 0)
|
|
256
|
0 |
0 |
if ($default_opt{'count-loops-by'} eq 'number-of-reads')
|
|
257
|
0 |
0 |
unless (defined $opts->{'number-of-reads'})
|
|
262
|
0 |
0 |
if (defined $opts->{'number-of-reads'} and $opts->{'number-of-reads'} <= 0)
|
|
266
|
0 |
0 |
unless (exists $OUTPUT_FORMAT{$opts->{'output-format'}})
|
|
271
|
0 |
0 |
unless ($opts->{'compression-level'} =~ /^[1-9]$/u)
|
|
276
|
0 |
0 |
unless (exists $SEQID_WEIGHT{$opts->{'seqid-weight'}})
|
|
282
|
0 |
0 |
if ($opts->{'expression-matrix'})
|
|
287
|
0 |
0 |
if ($opts->{'seqid-weight'} eq 'count')
|
|
288
|
0 |
0 |
unless (defined $opts->{'expression-matrix'})
|
|
293
|
0 |
0 |
unless (%EXPRESSION_MATRIX and exists $EXPRESSION_MATRIX{$opts->{'expression-matrix'}})
|
|
314
|
0 |
0 |
if ($default_opt{'count-loops-by'} eq 'coverage') { }
|
|
|
0 |
0 |
elsif ($default_opt{'count-loops-by'} eq 'number-of-reads') { }
|
|
315
|
0 |
0 |
if exists $opts->{'number-of-reads'}
|
|
318
|
0 |
0 |
if exists $opts->{'coverage'}
|
|
324
|
0 |
0 |
if ($opts->{'expression-matrix'})
|
|
329
|
0 |
0 |
if ($opts->{'quality-profile'} ne 'poisson')
|
|
334
|
0 |
0 |
if $entry->{'type'} eq 'single-molecule'
|
|
340
|
0 |
0 |
$opts->{'sequencing-type'} eq 'paired-end' ? :
|
|
343
|
0 |
0 |
if defined $opts->{'append-id'}
|
|
346
|
0 |
0 |
if ($opts->{'output-format'} =~ /^(bam|sam)$/u)
|
|
351
|
0 |
0 |
if ($opts->{'output-format'} =~ /fastq/u and $opts->{'sequencing-type'} eq 'paired-end' and $opts->{'join-paired-ends'})
|
|
354
|
0 |
0 |
unless $opts->{'id'} =~ /%R/u
|
|
358
|
0 |
0 |
if ($opts->{'genomic-variation'})
|
|
365
|
0 |
0 |
if ($opts->{'genomic-variation-regex'})
|
|
373
|
0 |
0 |
if (/$pattern/u)
|
|
381
|
0 |
0 |
if ($opts->{'genomic-variation'})
|
|
393
|
0 |
0 |
if (@$err_list)
|
|
443
|
0 |
0 |
if ($opts->{'sequencing-type'} eq 'paired-end') { }
|