| line |
!l |
l&&!r |
l&&r |
condition |
|
97
|
0 |
0 |
0 |
not $is_stranded and defined $chimeras{$reverse_key} |
|
212
|
0 |
0 |
0 |
$splice->{'type'} eq 'coverless' and not $coverless_splices |
|
339
|
0 |
0 |
0 |
defined $crac_version and &CracTools::Utils::isVersionGreaterOrEqual($crac_version, '2.4.0') |
|
372
|
0 |
0 |
0 |
defined $crac_version and not &CracTools::Utils::isVersionGreaterOrEqual($crac_version, '2.4.0') |
|
378
|
0 |
0 |
0 |
defined $crac_version and &CracTools::Utils::isVersionGreaterOrEqual($crac_version, '2.4.0') |
|
494
|
0 |
0 |
0 |
defined $ref_file and not defined $seq |
|
520
|
0 |
0 |
0 |
not $is_stranded and defined $chimera->{$reverse_key} |
|
|
0 |
0 |
0 |
$is_stranded and $line->isFlagged($CracTools::SAMReader::SAMline::flags{'FIRST_SEGMENT'}) |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
200
|
0 |
0 |
0 |
$line->isFlagged(256) || $line->isFlagged(2048) |
|
209
|
0 |
0 |
0 |
$splice->{'loc'}{'pos'} >= $region_end or $splice->{'loc'}{'pos'} < $region_start |
|
|
0 |
0 |
0 |
$splice->{'loc'}{'pos'} >= $region_end or $splice->{'loc'}{'pos'} < $region_start or $splice->{'loc'}{'chr'} ne $region_chr |
|
|
0 |
0 |
0 |
$splice->{'loc'}{'pos'} >= $region_end or $splice->{'loc'}{'pos'} < $region_start or $splice->{'loc'}{'chr'} ne $region_chr or $splice->{'gap'} < $min_gap_length |
|
285
|
0 |
0 |
0 |
$line->isFlagged(256) || $line->isFlagged(2048) |
|
292
|
0 |
0 |
0 |
$pos >= $region_end or $pos < $region_start |
|
331
|
0 |
0 |
0 |
$pos >= $region_end or $pos < $region_start |
|
366
|
0 |
0 |
0 |
$pos >= $region_end or $pos < $region_start |
|
511
|
0 |
0 |
0 |
$line->isFlagged(256) || $line->isFlagged(2048) |