| line |
true |
false |
branch |
|
40
|
0 |
0 |
if @$args < 1 |
|
42
|
0 |
0 |
if $name =~ /^-/ |
|
58
|
0 |
0 |
defined $opt->{'p'} ? : |
|
61
|
0 |
0 |
unless defined $bam_file |
|
67
|
0 |
0 |
if (@regions == 0) |
|
72
|
0 |
0 |
unless $line =~ /^\@SQ/ |
|
91
|
0 |
0 |
if (defined $data_structure_reference) |
|
97
|
0 |
0 |
if (not $is_stranded and defined $chimeras{$reverse_key}) |
|
100
|
0 |
0 |
if (defined $chimeras{$chim_key}) { } |
|
102
|
0 |
0 |
if defined $region_chimeras->{$key}{'score'} |
|
105
|
0 |
0 |
if defined $region_chimeras->{$key}{'score'} |
|
119
|
0 |
0 |
if $pm->start |
|
122
|
0 |
0 |
if defined $splices_file |
|
123
|
0 |
0 |
if defined $mutations_file |
|
133
|
0 |
0 |
if defined $splices_fh |
|
142
|
0 |
0 |
if defined $mutations_fh |
|
152
|
0 |
0 |
if defined $chimeras_file |
|
160
|
0 |
0 |
if defined $splices_fh |
|
161
|
0 |
0 |
if defined $mutations_fh |
|
166
|
0 |
0 |
if defined $chimeras_file |
|
167
|
0 |
0 |
if defined $chimeras_fh |
|
168
|
0 |
0 |
if defined $chimeras_fh |
|
171
|
0 |
0 |
if defined $splices_file |
|
172
|
0 |
0 |
if defined $mutations_file |
|
174
|
0 |
0 |
if defined $splices_fh |
|
175
|
0 |
0 |
if defined $mutations_fh |
|
183
|
0 |
0 |
if (defined $splices_file) |
|
188
|
0 |
0 |
if (defined $mutations_file) |
|
200
|
0 |
0 |
if (not $line->isFlagged(256) || $line->isFlagged(2048)) |
|
209
|
0 |
0 |
if $splice->{'loc'}{'pos'} >= $region_end or $splice->{'loc'}{'pos'} < $region_start or $splice->{'loc'}{'chr'} ne $region_chr or $splice->{'gap'} < $min_gap_length |
|
212
|
0 |
0 |
if $splice->{'type'} eq 'coverless' and not $coverless_splices |
|
222
|
0 |
0 |
if (not defined $splices->{$key}) { } |
|
232
|
0 |
0 |
if ($is_stranded) { } |
|
233
|
0 |
0 |
if ($line->isFlagged($CracTools::SAMReader::SAMline::flags{'FIRST_SEGMENT'})) { } |
|
254
|
0 |
0 |
if $splices->{$key}{'max'} < $max_pos |
|
255
|
0 |
0 |
if $splices->{$key}{'min'} < $line->pos |
|
265
|
0 |
0 |
unless $CracTools::App::Command::Extract::a->{'chr'} cmp $CracTools::App::Command::Extract::b->{'chr'} |
|
285
|
0 |
0 |
if (not $line->isFlagged(256) || $line->isFlagged(2048)) |
|
292
|
0 |
0 |
if $pos >= $region_end or $pos < $region_start |
|
295
|
0 |
0 |
if ($snp->{'actual'} eq '?') { } |
|
|
0 |
0 |
elsif ($snp->{'expected'} eq '?') { } |
|
331
|
0 |
0 |
if $pos >= $region_end or $pos < $region_start |
|
339
|
0 |
0 |
if (defined $crac_version and &CracTools::Utils::isVersionGreaterOrEqual($crac_version, '2.4.0')) |
|
366
|
0 |
0 |
if $pos >= $region_end or $pos < $region_start |
|
372
|
0 |
0 |
if (defined $crac_version and not &CracTools::Utils::isVersionGreaterOrEqual($crac_version, '2.4.0')) |
|
378
|
0 |
0 |
if (defined $crac_version and &CracTools::Utils::isVersionGreaterOrEqual($crac_version, '2.4.0')) { } |
|
405
|
0 |
0 |
unless $CracTools::App::Command::Extract::a->{'chr'} cmp $CracTools::App::Command::Extract::b->{'chr'} |
|
430
|
0 |
0 |
if (defined $mut) { } |
|
434
|
0 |
0 |
if ($mut->{'reference'} ne $args{'reference'}) |
|
438
|
0 |
0 |
if (length $args{'reference'} < length $mut->{'reference'}) { } |
|
|
0 |
0 |
elsif (length $args{'reference'} > length $mut->{'reference'}) { } |
|
459
|
0 |
0 |
if (defined $MUTATIONS->{$key}{'alternative'}{$args{'alternative'}}) { } |
|
471
|
0 |
0 |
if $MUTATIONS->{$key}{'total'} == 0 |
|
477
|
0 |
0 |
unless defined $pos2 |
|
494
|
0 |
0 |
if (defined $ref_file and not defined $seq) |
|
498
|
0 |
0 |
if defined $seq |
|
502
|
0 |
0 |
unless (defined $seq) |
|
511
|
0 |
0 |
if (not $line->isFlagged(256) || $line->isFlagged(2048)) |
|
520
|
0 |
0 |
if (not $is_stranded and defined $chimera->{$reverse_key}) { } |
|
|
0 |
0 |
elsif ($is_stranded and $line->isFlagged($CracTools::SAMReader::SAMline::flags{'FIRST_SEGMENT'})) { } |
|
526
|
0 |
0 |
if (defined $chimeras->{$key}) { } |
|
528
|
0 |
0 |
if defined $chimera->{'score'} |
|
531
|
0 |
0 |
if defined $chimera->{'score'} |
|
553
|
0 |
0 |
defined $chimeras->{$chim_key}{'score'} ? : |