| line |
true |
false |
branch |
|
62
|
1138 |
0 |
defined first(sub {
$needle eq $_;
}
, @_) ? : |
|
154
|
0 |
6 |
unless $agpfile |
|
156
|
0 |
6 |
if ($opt{'validate_identifiers'}) |
|
165
|
0 |
6 |
if (is_filehandle($agpfile)) { } |
|
168
|
0 |
6 |
unless open my $f, $agpfile |
|
177
|
0 |
0 |
unless $opt{'validate_syntax'} |
|
182
|
0 |
0 |
if ($opt{'error_array'}) { } |
|
203
|
4 |
642 |
if ($line =~ /#/) |
|
204
|
4 |
0 |
if ($line =~ s/^#//) |
|
213
|
0 |
642 |
unless @fields == 9 |
|
217
|
0 |
642 |
unless @fields >= 5 and @fields <= 10 |
|
223
|
0 |
642 |
unless $r{'objname'} |
|
226
|
636 |
0 |
if (defined $last_end and defined $last_objname and $r{'objname'} eq $last_objname) |
|
227
|
0 |
636 |
unless $r{'ostart'} == $last_end + 1 |
|
234
|
0 |
642 |
unless $r{'oend'} >= $r{'ostart'} |
|
238
|
0 |
642 |
unless $r{'partnum'} == $last_partnum + 1 |
|
244
|
496 |
146 |
if ($r{'type'} =~ /^[NU]$/) { } |
|
|
146 |
0 |
elsif ($r{'type'} =~ /^[ADFGOPW]$/) { } |
|
248
|
0 |
496 |
unless $r{'typedesc'} = $descmap{$r{'type'}} |
|
254
|
0 |
496 |
unless $r{'length'} == $r{'oend'} - $r{'ostart'} + 1 |
|
257
|
0 |
496 |
unless str_in($r{'gap_type'}, ('fragment', 'clone', 'contig', 'centromere', 'short_arm', 'heterochromatin', 'telomere', 'repeat')) |
|
260
|
0 |
496 |
unless str_in($r{'linkage'}, ('yes', 'no')) |
|
263
|
0 |
496 |
unless defined $empty and $empty eq '' |
|
270
|
0 |
146 |
unless $r{'typedesc'} = $descmap{$r{'type'}} |
|
275
|
0 |
146 |
if ($opt{'validate_identifiers'}) { } |
|
276
|
0 |
0 |
unless my $comp_type = identifier_namespace($r{'ident'}) |
|
279
|
0 |
146 |
unless $r{'ident'} |
|
282
|
0 |
146 |
unless str_in($r{'orient'}, ('+', '-', '0', 'na')) |
|
285
|
0 |
146 |
unless $r{'cstart'} >= 1 and $r{'cend'} > $r{'cstart'} |
|
290
|
0 |
146 |
unless $r{'length'} == $r{'oend'} - $r{'ostart'} + 1 |
|
299
|
0 |
6 |
if $parse_error_flag |
|
323
|
0 |
3 |
unless $file |
|
326
|
3 |
0 |
is_filehandle($file) ? : |
|
327
|
0 |
0 |
unless open my $f, ">$file" |
|
348
|
2 |
321 |
if $$line{'comment'} |
|
352
|
248 |
73 |
if ($$line{'type'} =~ /^[NU]$/) { } |
|
380
|
2 |
321 |
if $$l{'comment'} |
|
381
|
248 |
73 |
if ($$l{'typedesc'} =~ /_gap$/) { } |
|
382
|
42 |
206 |
if @{$contigs[-1];} |
|
387
|
2 |
1 |
if @{$contigs[-1];} == 0 |