| line |
true |
false |
branch |
|
108
|
0 |
0 |
$infile->exists ? : |
|
118
|
0 |
3 |
if ($tool eq 'soap') { } |
|
|
3 |
0 |
elsif ($tool eq 'bwa') { } |
|
120
|
0 |
0 |
unless -e "$genome.index.$suffix" |
|
124
|
5 |
10 |
unless -e "$genome.bwa.$suffix" |
|
135
|
0 |
1 |
unless -e $genome |
|
139
|
1 |
0 |
$tool eq 'bwa' ? : |
|
|
0 |
1 |
$tool eq 'soap' ? : |
|
142
|
1 |
0 |
if (@cmd) |
|
145
|
0 |
1 |
unless run(\@cmd, \$in, \$out, \$err) |
|
147
|
1 |
0 |
$self->exist_index ? : |
|
159
|
0 |
1 |
if $self->exist_index == 0 or $self->force_index |
|
160
|
1 |
0 |
$tool eq 'bwa' ? : |
|
|
0 |
1 |
$tool eq 'soap' ? : |
|
164
|
0 |
1 |
if ($tool eq 'soap') { } |
|
|
1 |
0 |
elsif ($tool eq 'bwa') { } |
|
167
|
0 |
0 |
unless run(\@cmd, \$in, \$out, \$err) |
|
168
|
0 |
0 |
$err ? : |
|
172
|
0 |
1 |
unless run(\@cmd, \$in, \$out, \$err) |
|
176
|
0 |
1 |
unless run(\@cmd, \$in, \$out, \$err) |
|
186
|
0 |
1 |
if ($indir) { } |
|
|
1 |
0 |
elsif ($infile) { } |
|
188
|
0 |
0 |
unless @fqs |
|
189
|
0 |
0 |
unless -e $outdir |
|
193
|
0 |
0 |
if my $pid = $pm->start |
|
200
|
0 |
1 |
unless -e $infile |
|
211
|
0 |
1 |
unless $outfile->exists |
|
213
|
0 |
1 |
if ($tool eq 'soap') { } |
|
|
1 |
0 |
elsif ($tool eq 'bwa') { } |
|
216
|
0 |
0 |
unless $cols[3] == 1 |
|
217
|
0 |
0 |
if $cols[9] == 0 |
|
218
|
0 |
0 |
if $cols[9] =~ /^[01]$/u |
|
219
|
0 |
0 |
if $cols[9] =~ /^[012]$/u |
|
224
|
5 |
7 |
if $line =~ /^@/u |
|
225
|
1 |
6 |
if @cols == 11 |
|
226
|
0 |
6 |
unless $cols[11] eq 'XT:A:U' |
|
227
|
6 |
0 |
if $cols[12] eq 'NM:i:0' |
|
228
|
6 |
0 |
if $cols[12] =~ /NM:i:[01]/u |
|
229
|
6 |
0 |
if $cols[12] =~ /NM:i:[012]/u |