| line |
true |
false |
branch |
|
221
|
0 |
0 |
unless (grep /command/, @args) |
|
226
|
0 |
0 |
unless defined $self->program_name |
|
249
|
0 |
0 |
unless ($HAVE_SAMTOOLS) |
|
252
|
0 |
0 |
unless $rd1_file |
|
253
|
0 |
0 |
unless $ref_file |
|
255
|
0 |
0 |
unless $_ |
|
256
|
0 |
0 |
if (/\.gz[^.]*$/) |
|
257
|
0 |
0 |
unless ($HAVE_IO_UNCOMPRESS) |
|
270
|
0 |
0 |
unless $guesser->guess eq 'fastq' |
|
272
|
0 |
0 |
unless $guesser->guess eq 'fasta' |
|
273
|
0 |
0 |
if ($rd2_file) |
|
275
|
0 |
0 |
unless $guesser->guess eq 'fastq' |
|
281
|
0 |
0 |
if ($HAVE_SAMTOOLS) |
|
291
|
0 |
0 |
unless $samt->run(-'bam', $nm . $suf, -'out', $bam_file) |
|
293
|
0 |
0 |
unless $samt->run(-'bam', $bam_file, -'pfx', $nm . '.srt') |
|
325
|
0 |
0 |
if $self->can('command') |
|
326
|
0 |
0 |
unless $cmd |
|
329
|
0 |
0 |
unless $filespec |
|
333
|
0 |
0 |
if @args % 2 |
|
347
|
0 |
0 |
if (/^1?>(.*)/) |
|
348
|
0 |
0 |
if defined $args{$1} |
|
351
|
0 |
0 |
if (/^2>#?(.*)/) |
|
352
|
0 |
0 |
if defined $args{$1} |
|
355
|
0 |
0 |
if (/^<#?(.*)/) |
|
356
|
0 |
0 |
if defined $args{$1} |
|
361
|
0 |
0 |
unless $in |
|
362
|
0 |
0 |
unless $out |
|
363
|
0 |
0 |
unless $err |
|
379
|
0 |
0 |
if ref $files[$_] eq 'ARRAY' |
|
381
|
0 |
0 |
defined $_ ? : |
|
385
|
0 |
0 |
unless IPC::Run::run(\@ipc_args, $in, $out, $err) |
|
388
|
0 |
0 |
if ($@) |
|
411
|
0 |
0 |
if @_ |
|
430
|
0 |
0 |
if @_ |
|
501
|
0 |
0 |
if defined $self->$opt |
|
528
|
0 |
0 |
if $paired |
|
532
|
0 |
0 |
if $paired |
|
549
|
0 |
0 |
if $paired |
|
554
|
0 |
0 |
$paired ? : |
|
|
0 |
0 |
$paired ? : |
|
556
|
0 |
0 |
if ($paired) { } |
|
589
|
0 |
0 |
unless (defined $_) |
|
592
|
0 |
0 |
if (/^c/i) |
|
595
|
0 |
0 |
if (/^f/i) |