| line |
true |
false |
branch |
|
239
|
0 |
1 |
unless (grep /command/, @args) |
|
244
|
1 |
0 |
unless defined $self->program_name |
|
245
|
0 |
1 |
if ($^O =~ /cygwin/) |
|
276
|
0 |
0 |
unless $rd1_file |
|
277
|
0 |
0 |
unless $ref_file |
|
280
|
0 |
0 |
unless $_ |
|
281
|
0 |
0 |
if (/\.gz[^.]*$/) |
|
282
|
0 |
0 |
unless ($HAVE_IO_UNCOMPRESS) |
|
294
|
0 |
0 |
unless $guesser->guess eq 'fastq' |
|
296
|
0 |
0 |
unless $guesser->guess eq 'fasta' |
|
297
|
0 |
0 |
if ($rd2_file) |
|
299
|
0 |
0 |
unless $guesser->guess eq 'fastq' |
|
330
|
0 |
0 |
if $self->can('command') |
|
331
|
0 |
0 |
unless $cmd |
|
334
|
0 |
0 |
unless $filespec |
|
338
|
0 |
0 |
if @args % 2 |
|
352
|
0 |
0 |
if (/^1?>(.*)/) |
|
353
|
0 |
0 |
if defined $args{$1} |
|
356
|
0 |
0 |
if (/^2>#?(.*)/) |
|
357
|
0 |
0 |
if defined $args{$1} |
|
360
|
0 |
0 |
if (/^<#?(.*)/) |
|
361
|
0 |
0 |
if defined $args{$1} |
|
366
|
0 |
0 |
unless $in |
|
367
|
0 |
0 |
unless $out |
|
368
|
0 |
0 |
unless $err |
|
384
|
0 |
0 |
if ref $files[$_] eq 'ARRAY' |
|
386
|
0 |
0 |
defined $_ ? : |
|
390
|
0 |
0 |
unless IPC::Run::run(\@ipc_args, $in, $out, $err) |
|
393
|
0 |
0 |
if ($@) |
|
416
|
0 |
0 |
if @_ |
|
435
|
0 |
0 |
if @_ |
|
473
|
0 |
0 |
if (grep /^-/, @args) { } |
|
474
|
0 |
0 |
if @args % 2 |
|
482
|
0 |
0 |
unless defined $read1 and defined $refseq |
|
484
|
0 |
0 |
unless -e $read1 and -e $refseq and !defined($read2) || -e $read2 |
|
498
|
0 |
0 |
if (defined $read2) |
|
541
|
0 |
0 |
if defined $self->$opt |
|
631
|
1 |
2 |
unless (defined $_) |
|
634
|
0 |
2 |
if (/^c/i) |
|
637
|
0 |
2 |
if (/^f/i) |