| line |
true |
false |
branch |
|
115
|
0 |
0 |
unless defined $args->{'-max_target_seqs'}
|
|
124
|
0 |
0 |
if $query_seqs->type eq 'prot' and $blastdb->type eq 'nucl'
|
|
139
|
0 |
0 |
unless $rp->debug_mode
|
|
164
|
0 |
0 |
if ($rp->ref_brh eq 'off')
|
|
181
|
0 |
0 |
if $homologous_seqs->type eq 'nucl' and $blastdb->type eq 'prot'
|
|
191
|
0 |
0 |
if $in_best_hits
|
|
193
|
0 |
0 |
unless $rp->debug_mode
|
|
207
|
0 |
0 |
unless ($rp->run_mode eq 'metagenomic')
|
|
208
|
0 |
0 |
if ($rp->merge_orthologues eq 'on')
|
|
227
|
0 |
0 |
unless $blastdb
|
|
234
|
0 |
0 |
if $orthologous_seqs->type eq 'nucl' and $blastdb->type eq 'prot'
|
|
249
|
0 |
0 |
unless $rp->debug_mode
|
|
263
|
0 |
0 |
unless $blastdb
|
|
270
|
0 |
0 |
if $orthologous_seqs->type eq 'nucl' and $blastdb->type eq 'prot'
|
|
277
|
0 |
0 |
unless $bo
|
|
283
|
0 |
0 |
unless $orthologue->count_hits
|
|
296
|
0 |
0 |
if $self->is_allowed($hit_id)
|
|
305
|
0 |
0 |
unless $rp->debug_mode
|
|
325
|
0 |
0 |
if $orthologous_seqs->type eq 'nucl' and $blastdb->type eq 'prot'
|
|
334
|
0 |
0 |
unless $bo
|
|
338
|
0 |
0 |
unless ($orthologue->count_hits)
|
|
346
|
0 |
0 |
unless $tax_line
|
|
351
|
0 |
0 |
if $contam_org
|
|
365
|
0 |
0 |
if $rp->run_mode eq 'metagenomic'
|
|
368
|
0 |
0 |
if ($rp->aligner_mode eq 'off')
|
|
392
|
0 |
0 |
if ($rp->ali_skip_self eq 'on')
|
|
393
|
0 |
0 |
if ($template_id->full_org eq $transcript_seq->full_org)
|
|
405
|
0 |
0 |
if $coverage < $best_coverage * $rp->ali_cover_mul
|
|
421
|
0 |
0 |
unless (@templates)
|
|
429
|
0 |
0 |
if ($rp->aligner_mode =~ /exonerate|exoblast/msx)
|
|
450
|
0 |
0 |
if ($new_seq->seq_len) { }
|
|
451
|
0 |
0 |
$rp->aligner_mode eq 'exoblast' ? :
|
|
473
|
0 |
0 |
if ($rp->aligner_mode eq 'blast' or $rp->aligner_mode eq 'exoblast' and $failure)
|
|
481
|
0 |
0 |
unless $template_seq
|
|
504
|
0 |
0 |
if ($ap->query_seqs->type eq 'nucl' and $blastdb->type eq 'nucl' and $hsp->hit_strand == -1)
|
|
529
|
0 |
0 |
unless $rp->debug_mode
|
|
549
|
0 |
0 |
unless @seqs2cap
|
|
556
|
0 |
0 |
if (@seqs2cap < 2)
|
|
578
|
0 |
0 |
unless @contigs
|
|
619
|
0 |
0 |
if not defined $end and defined $start and $start =~ /\A \+\d+ \z/msx
|
|
632
|
0 |
0 |
if ($ap->para_blastdb)
|
|
634
|
0 |
0 |
if ($para_score > $temp_score)
|
|
641
|
0 |
0 |
if ($rp->tol_blastdb)
|
|
643
|
0 |
0 |
if ($tol_score > $temp_score)
|
|
660
|
0 |
0 |
if $family
|
|
679
|
0 |
0 |
if ($rp->tax_reports eq 'on' or $self->_tax_filter)
|
|
706
|
0 |
0 |
if @relatives >= $rp->tax_max_hits
|
|
718
|
0 |
0 |
unless $tax
|
|
720
|
0 |
0 |
if $score < $rp->tax_min_score
|
|
721
|
0 |
0 |
if $score < $rp->tax_score_mul * $best_score
|
|
725
|
0 |
0 |
if $len < $rp->tax_min_len
|
|
727
|
0 |
0 |
if $ident < $rp->tax_min_ident
|
|
733
|
0 |
0 |
if (@taxonomy)
|
|
748
|
0 |
0 |
if (@relatives < $rp->tax_min_hits) { }
|
|
751
|
0 |
0 |
if ($self->_tax_filter)
|
|
764
|
0 |
0 |
if ($rp->tax_reports eq 'on')
|
|
773
|
0 |
0 |
if ($self->_tax_filter and $rp->tol_check eq 'off')
|
|
775
|
0 |
0 |
unless ($self->is_allowed($common_tax))
|
|
789
|
0 |
0 |
if ($count > 1)
|
|
796
|
0 |
0 |
if $more
|
|
801
|
0 |
0 |
$org =~ /$Bio::MUST::Apps::FortyTwo::OrgProcessor::PKEYONLY/ || $org =~ /$Bio::MUST::Apps::FortyTwo::OrgProcessor::GCAONLY/ ? :
|
|
835
|
0 |
0 |
if ($self->tax_filter)
|
|
837
|
0 |
0 |
if $tax
|
|
842
|
0 |
0 |
unless $self->homologous_seqs->all_long_ids
|
|
845
|
0 |
0 |
unless $self->orthologous_seqs->all_long_ids
|
|
848
|
0 |
0 |
unless $self->aligned_seqs->all_seq_ids
|